Merge remote-tracking branch 'origin/master' into feat/parallel-sync

# Conflicts:
#	CHANGELOG.md
#	CLAUDE.md
#	VERSION
#	llms-full.txt
#	package.json
#	src/commands/sync.ts

.github/workflows/test.yml

@@ -21,11 +21,22 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
   test:
+    # ubuntu-latest is free 2-core/7GB. Larger runners (16-cores, etc.) require
+    # a provisioned runner pool in repo settings. Falling back to default keeps
+    # the matrix shard speedup (~5-6x via parallelism) at zero cost.
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: [1, 2, 3, 4]
     steps:
       - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: latest
       - run: bun install
-      - run: bun run test
+      - name: Pre-test gates (shard 1 only — they're not test files)
+        if: matrix.shard == 1
+        run: scripts/check-jsonb-pattern.sh && scripts/check-progress-to-stdout.sh && scripts/check-wasm-embedded.sh && bun run typecheck
+      - name: Run test shard ${{ matrix.shard }}/4
+        run: scripts/test-shard.sh ${{ matrix.shard }} 4

.gitignore

@@ -17,3 +17,4 @@ eval/data/world-v1/world.html
 
 # BrainBench amara-life-v1 Opus cache (regenerate via eval:generate-amara-life)
 eval/data/amara-life-v1/_cache/
+.claude/

CHANGELOG.md

@@ -2,6 +2,544 @@
 
 All notable changes to GBrain will be documented in this file.
 
+## [0.22.13] - 2026-04-28
+
+**Sync got faster, and the bookmark stopped lying.**
+**Parallel imports, a real writer lock, and a head-drift gate that catches the worst race.**
+
+The headline is `gbrain sync --workers N`: per-worker Postgres engines with an atomic queue index, same pattern as `gbrain import --workers N`. On a 7,000-page brain that used to take 25+ minutes, the import phase now runs across 4 workers by default. The reproducible benchmark in `test/e2e/sync-parallel.test.ts` shows `parallel(4)` finishing 1.3× faster than serial on a 120-file fixture against local Postgres (`serial=289ms parallel(4)=221ms`). The speedup grows on larger brains and slower-roundtrip databases (Supabase, remote PgBouncer) because the worker setup cost amortizes over more files. But the bigger story is that the sync writer is finally exclusive across processes, and the `last_commit` bookmark refuses to advance when git HEAD has drifted out from under us. The silent-skip-then-advance pathology has survived every prior sync hardening pass. It is dead now.
+
+### What you can do now
+
+- `gbrain sync --workers 4` (alias `--concurrency 4`) parallelizes the import phase. Each worker holds 2 connections, so total Postgres connections during the parallel phase is `workers * 2` plus your caller's pool. At the default of 4 workers and a 10-connection caller pool, that's up to 18 connections, well under PgBouncer's `max_client_conn` default of 100 but worth knowing on tight Supabase tiers.
+- **Auto-concurrency:** if you don't pass `--workers`, sync uses 4 workers when the diff exceeds 100 files. Smaller diffs stay serial. Explicit `--workers` always wins (even on a 30-file diff). PGLite forces serial regardless, since it's a single-connection engine.
+- **Full sync** routes through the same path. First syncs on large brains parallelize automatically.
+- **Minion `sync` jobs** also use the new `autoConcurrency()` policy. Behavior is now consistent between CLI sync, the Minion handler, and the autopilot cycle's sync phase. (`noEmbed` defaults to `true` in the jobs handler. Submit `gbrain embed --stale` as a separate job when needed, or rely on the autopilot cycle's embed phase.)
+- **`--workers` validation is loud now.** `--workers 0`, `--workers -3`, `--workers foo`, `--workers 1.5` all exit with an error message. The prior behavior silently fell through to auto-concurrency (4 workers), the opposite of what you typed.
+
+### Correctness fixes you didn't have to ask for
+
+- **Cross-process writer lock.** Two `gbrain sync` calls (manual + autopilot, two terminals, two Conductor workspaces) used to read the same `last_commit`, both write it, and let the last writer win. The new `gbrain-sync` row in `gbrain_cycle_locks` serializes the writer window. Same-process reentrance from the autopilot cycle handler was already covered by the broader `gbrain-cycle` lock; sync's lock is narrower and runs underneath it.
+- **Head-drift gate.** If `git checkout` or `git pull` runs in your worktree mid-sync (Conductor sibling workspace, ad-hoc terminal), the captured `headCommit` no longer matches HEAD when sync finishes. `last_commit` no longer advances in that case. The next sync re-walks the diff against the new HEAD instead of silently moving the bookmark past unimported work.
+- **Vanished files now block bookmark advance.** A file the diff said exists at `headCommit` but is gone from disk used to register as a benign skip. It now goes into `failedFiles` and gates `last_commit` the same way a parse failure does.
+- **Per-source bookmark for Minion `sync` jobs.** The job handler now resolves `sourceId` from the repo path (mirrors the autopilot cycle's `cycle.ts` fix from PR #475). On multi-source brains, this prevents the 30-min full-reimport-every-cycle behavior caused by reading the global `config.sync.last_commit` anchor when the per-source row would have been correct.
+- **Worker connection cleanup.** Worker engines now disconnect inside `try/finally`, even on partial connect failure or mid-import error. The prior `Promise.all(...disconnect)` ran outside any try/finally, so panic-path leaks never released the 8 worker connections.
+- **Engine detection unified.** Both PGLite-detection sites in sync.ts now use `engine.kind === 'pglite'` (the discriminator added in v0.13.1). The `engine.constructor.name === 'PGLiteEngine'` sniff is gone, since it broke under bundling and was inconsistent with the other site's `config.engine` string check.
+
+### What this means for you
+
+If you run autopilot on a 7,000-page Postgres brain, your sync cycle gets faster on day one with no flags. If you have ever felt the bookmark "skip past" work that didn't import, you'll stop seeing it. If you have multiple Conductor workspaces poking the same brain, you'll either wait politely on the writer lock or get a clear "another sync is in progress" error. None of this requires a config change.
+
+## To take advantage of v0.22.13
+
+`gbrain upgrade` should do this automatically. If you want to use the new flags right now:
+
+1. **For a one-off speed win on a large brain:**
+   ```bash
+   gbrain sync --workers 4
+   ```
+   Or for incremental syncs that touch >100 files, just run `gbrain sync`. Auto-concurrency fires.
+
+2. **For your autopilot cycle:** no action. The Minion `sync` handler picks up the new auto-concurrency policy automatically.
+
+3. **Verify the writer lock is working:**
+   ```bash
+   gbrain sync &
+   gbrain sync   # second call will say "Another sync is in progress" or wait
+   ```
+
+4. **If sync ever errors with "Another sync is in progress" and stays stuck:** the lock is in `gbrain_cycle_locks` with id `gbrain-sync` and a 30-minute TTL. If a worker crashed without releasing, the next acquirer takes over once the TTL expires. To unstick faster:
+   ```sql
+   DELETE FROM gbrain_cycle_locks WHERE id = 'gbrain-sync';
+   ```
+
+5. **If anything looks wrong,** file an issue: https://github.com/garrytan/gbrain/issues with output of `gbrain doctor` and the contents of `~/.gbrain/upgrade-errors.jsonl` if it exists.
+
+### Itemized changes
+
+- `src/commands/sync.ts`: `performSync` now wraps body in a `gbrain-sync` DB lock; `--workers` honored regardless of file count when explicit; head-drift gate after import phase; engine.kind detection; try/finally around worker engines; banner moved to stderr.
+- `src/commands/import.ts`: `engine.kind === 'pglite'` discriminator; try/finally around worker engines; shared `parseWorkers()` for `--workers` validation.
+- `src/commands/jobs.ts`: sync handler resolves `sourceId` via `sources.local_path` lookup; concurrency routed through `autoConcurrency()`; `noEmbed: true` default documented.
+- `src/core/sync-concurrency.ts` (new): `autoConcurrency()` + `parseWorkers()` + constants. One source of truth for the concurrency policy that previously lived in three call sites.
+- `src/core/db-lock.ts` (new): generic `tryAcquireDbLock(engine, lockId)` over the existing `gbrain_cycle_locks` table. Reused by performSync. cycle.ts continues to use its own ID `gbrain-cycle` so the two locks nest cleanly.
+- `test/sync-concurrency.test.ts` (new): 17 cases covering autoConcurrency thresholds, shouldRunParallel gates, parseWorkers validation.
+- `test/sync-parallel.test.ts` (new): PGLite-routed coverage of the bookmark gate under concurrency request, the head-drift gate, the writer-lock contract, and PGLite-stays-serial.
+- `test/e2e/sync-parallel.test.ts` (new): DATABASE_URL-gated Postgres E2E. 60-file happy path with `pg_stat_activity` leak probe, plus a 120-file serial-vs-parallel benchmark that prints `SYNC_PARALLEL_BENCH ...` for CHANGELOG quoting.
+
+### For contributors
+
+- `BrainEngine.kind` is now the canonical PGLite/Postgres discriminator. Avoid `engine.constructor.name === '...'` (breaks under bundling) and `config.engine === '...'` (inconsistent with the engine actually in use).
+- The `gbrain_cycle_locks` table is now multi-purpose. The id column distinguishes lock scopes: `gbrain-cycle` for the cycle, `gbrain-sync` for the sync writer. Future locks should pick distinct ids and reuse `tryAcquireDbLock`.
+- `parseWorkers()` is the canonical CLI flag parser for `--workers`. Use it instead of inline `parseInt`.
+
+## [0.22.12] - 2026-04-29
+
+**`sync --skip-failed` now classifies file-size and symlink rejections instead of bucketing them as UNKNOWN.**
+**Plus a full end-to-end test for the failure loop.**
+
+v0.22.9 shipped the headline classifier work: code-grouped breakdowns at sync time,
+DB-vs-YAML disambiguation, doctor surfaces both unacked and historical entries with
+`[CODE=N]` lines. v0.22.12 closes the last two coverage gaps that v0.22.9 left on
+the table:
+
+- **FILE_TOO_LARGE** now covers the three real production sites in
+  `src/core/import-file.ts:199, 352, 401` ("Content too large", "File too large",
+  "Code file too large"). On v0.22.9 these all bucketed as UNKNOWN — the same
+  silent-systemic-failure pattern that motivated the original issue.
+- **SYMLINK_NOT_ALLOWED** covers `src/core/import-file.ts:347` ("Skipping symlink").
+  Security-relevant rejection that operators should see.
+- **End-to-end failure-loop test** in `test/e2e/sync.test.ts` exercises the full
+  chain: broken file → sync blocks with grouped breakdown → `--skip-failed`
+  advances bookmark with grouped acknowledgement → second broken file → second
+  cycle. PostgreSQL-backed; verifies bookmark gating, JSONL state, dedup, and
+  summary aggregation. v0.22.9's coverage was unit-tests-only.
+
+Twelve total error codes ship in the classifier:
+`SLUG_MISMATCH`, `YAML_PARSE`, `YAML_DUPLICATE_KEY`, `DB_DUPLICATE_KEY`,
+`MISSING_OPEN`, `MISSING_CLOSE`, `NESTED_QUOTES`, `EMPTY_FRONTMATTER`,
+`NULL_BYTES`, `INVALID_UTF8`, `STATEMENT_TIMEOUT`, `FILE_TOO_LARGE`,
+`SYMLINK_NOT_ALLOWED`. Anything the regex set doesn't recognize falls through
+as `UNKNOWN`.
+
+### What this means for you
+
+If your brain rejects oversized files or symlinks, you now see those rejections
+in the doctor breakdown and at sync time grouped by code, instead of as
+`UNKNOWN`. Run `gbrain upgrade`. No manual action required.
+
+### Itemized changes
+
+#### Added
+- `FILE_TOO_LARGE` classifier code covering `src/core/import-file.ts:199, 352, 401`.
+- `SYMLINK_NOT_ALLOWED` classifier code covering `src/core/import-file.ts:347`.
+- Two new unit tests in `test/sync-failures.test.ts` pinning the new codes against
+  literal production message strings (`File too large (N bytes)`, `Skipping symlink: ...`).
+- `test/e2e/sync.test.ts` — new failure-loop test exercising broken-file → block →
+  `--skip-failed` → second cycle. Hermetic on developer machines (saves+restores
+  the user's real `~/.gbrain/sync-failures.jsonl`).
+
+## To take advantage of v0.22.12
+
+No manual action required. Run `gbrain upgrade`. The new `FILE_TOO_LARGE` and
+`SYMLINK_NOT_ALLOWED` classifier codes apply on the next `gbrain sync`.
+
+## [0.22.11] - 2026-04-27
+
+**Storage tiering, finally working. Brains scaling past 100K files stop bloating git.**
+
+The original storage-tiering branch shipped two silent bugs (gray-matter on YAML returned empty data; `manageGitignore` was defined and never invoked) so the feature was a no-op for every user who tried it. v0.22.11 rewrites the broken bits, hardens the surface, and adds proper test coverage. If you have a brain repo north of 100K files where bulk machine-generated content (tweets, articles, transcripts) is the size driver, this is the release that pulls it out of git without losing any data.
+
+Configure tiering in `gbrain.yml` at the brain repo root:
+
+```yaml
+storage:
+  db_tracked:
+    - people/
+    - companies/
+    - deals/
+  db_only:
+    - media/x/
+    - media/articles/
+    - meetings/transcripts/
+```
+
+`gbrain sync` then auto-manages your `.gitignore` for `db_only` directories so bulk content stops landing in commits. `gbrain export --restore-only` repopulates missing `db_only` files from the database (container restart, fresh clone, accidental rm). `gbrain storage status` shows the breakdown — counts, disk usage, missing files.
+
+### The numbers that matter
+
+200K-page brain, half tweets and articles. Before v0.22.11:
+
+| Metric | Before | After | Δ |
+|--------|--------|-------|---|
+| `gbrain.yml` actually loads | no (silent null) | yes | feature works |
+| `.gitignore` auto-manages | no (function never called) | yes | docs match reality |
+| `--restore-only` without `--repo` | silent full export | hard error | no data-loss footgun |
+| `media/xerox` matched against `media/x` | yes (collision) | no | path-segment matching |
+| Per-page disk syscalls during status | ~400K (existsSync + statSync) | ~one per dir + one stat per .md | single-walk scan |
+| Validation surfaces overlap | warning only | throws StorageConfigError | semantic error caught |
+
+### What this means for your brain
+
+If you've been reading the storage-tiering docs and waiting for the feature to actually do something: it does now. If you're already over 50K files: configure `gbrain.yml`, run `gbrain sync`, watch `.gitignore` update itself, watch your next clone get faster.
+
+## To take advantage of v0.22.11
+
+1. Add a `storage:` section to `gbrain.yml` at your brain repo root with `db_tracked` and `db_only` arrays. The directory paths must end with `/` (the validator auto-normalizes if you forget, with a one-time info note).
+2. Run `gbrain sync`. It updates `.gitignore` automatically on success.
+3. Run `gbrain storage status` to see the tier breakdown and any missing `db_only` files.
+4. If files are missing on disk (e.g., after a container restart): `gbrain export --restore-only --repo /path/to/brain`.
+5. If you previously had `git_tracked` / `supabase_only` keys: they still load, with a once-per-process deprecation warning. Rename to `db_tracked` / `db_only` at your convenience.
+6. On PGLite: tiering has limited effect (the "DB" is your local file). The `.gitignore` housekeeping still helps. A one-time soft-warn explains.
+
+If anything looks off, file an issue at <https://github.com/garrytan/gbrain/issues> with `gbrain doctor` output and the contents of your `gbrain.yml`.
+
+### Itemized changes
+
+#### Critical fixes
+
+- **YAML parser swap**: replaced `gray-matter` with a dedicated YAML reader for the `gbrain.yml` shape. The original code called `matter()` on a delimiter-less file, which always returned `{data: {}}` — `loadStorageConfig` returned null on every install. The dedicated parser handles top-level `storage:` plus nested array-valued keys, with comment + blank-line tolerance. Once-per-process sanity warning when `gbrain.yml` exists but has no `storage:` section.
+- **`manageGitignore` actually runs now**: wired into `runSync` after every successful sync (skipped on dry-run, blocked-by-failures, and unhandled errors). Idempotent. Detects git submodule context (`.git` is a file, not a directory) and skips with an actionable warning. Honors `GBRAIN_NO_GITIGNORE=1` for shared-repo setups.
+- **No more silent `--restore-only` footgun**: `gbrain export --restore-only` without `--repo` now resolves through a typed `getDefaultSourcePath()` accessor (sources table → null → hard error). Never falls through to the current directory. Never silently re-exports your entire database into the wrong place.
+
+#### New + renamed surface
+
+- **Canonical key names**: `db_tracked` / `db_only` replace the vendor-baked `git_tracked` / `supabase_only`. The deprecated keys still load, with a once-per-process warning suggesting `gbrain doctor --fix` for an automated rename. Canonical wins when both shapes coexist.
+- **Engine-side `slugPrefix` filter**: `PageFilters.slugPrefix` lands on both engines as `WHERE slug LIKE prefix || '%'` with literal-escape of LIKE metacharacters. Uses the existing `(source_id, slug)` UNIQUE btree index for range scans. Powers `gbrain export --restore-only` per-tier queries and `gbrain export --slug-prefix`.
+- **Single-walk filesystem scan**: `src/core/disk-walk.ts` exposes `walkBrainRepo(repoPath)` that returns `Map<slug, {size, mtimeMs}>` from one recursive `readdirSync`. Replaces the per-page `existsSync + statSync` loop in `gbrain storage status` (~400K syscalls on a 200K-page brain → tens).
+- **Path-segment matching**: tier directory matcher requires trailing `/` and treats the slash as a path separator. `media/x/` does not match `media/xerox/foo`. Validator (`normalizeAndValidateStorageConfig`) auto-fixes missing trailing `/`, throws `StorageConfigError` on tier overlap.
+
+#### Architecture cleanup
+
+- `src/commands/storage.ts` split into pure data + JSON formatter + human formatter + thin dispatcher, matching the `orphans.ts` precedent. `getStorageStatus` is exported for `gbrain doctor` integration. ASCII-only output (no unicode box-drawing) for cross-platform terminal compatibility.
+- Distinct nominal types `PageCountsByTier` and `DiskUsageByTier` so accidental swaps between page counts and byte totals are compile-time errors.
+- PGLite soft-warn on storage tiering (D4): the feature is partial on PGLite (the "DB" is your local file), but `.gitignore` housekeeping still helps. Once-per-process warning explains and proceeds.
+
+#### Tests + CI guards
+
+- New unit tests across `test/storage-config.test.ts`, `test/storage-sync.test.ts`, `test/storage-status.test.ts`, `test/storage-export.test.ts`, `test/storage-pglite.test.ts`, `test/disk-walk.test.ts`. Plus extensions to `test/source-resolver.test.ts` and `test/pglite-engine.test.ts`. The single-line test that would have caught the original gray-matter P0 (write a real `gbrain.yml`, call `loadStorageConfig`, assert non-null) now exists.
+- New CI guard `scripts/check-trailing-newline.sh` (sibling to the existing jsonb-pattern + progress-to-stdout guards). Wired into `bun run test`. Fixed pre-existing missing newline in `docs/storage-tiering.md`.
+
+### For contributors
+
+- The eng-review path forward is documented in `~/.claude/plans/lets-take-a-look-ticklish-pizza.md` (15 numbered defects + D1-D8 abstraction calls). Every commit on this branch maps to one numbered step in the plan.
+
+## [0.22.10] - 2026-04-30
+
+**`gbrain jobs submit autopilot-cycle --params '{"phases":["lint","backlinks"]}'` now actually runs only those phases.**
+
+If you ever submitted an `autopilot-cycle` job with a `phases:` array hoping to skip embed for a fast cycle, you got the full 6-phase cycle anyway. The handler in `src/commands/jobs.ts` was calling `runCycle(...)` without forwarding `job.data.phases`, so per-cycle phase selection was silently ignored.
+
+This release wires the array through. The handler imports `ALL_PHASES` from `src/core/cycle.ts`, builds a `Set` for O(1) validation, and filters the caller's `phases` array against it before forwarding to `runCycle`. Invalid phase names get dropped (no injection surface — `ALL_PHASES` is the authoritative list). Empty arrays and non-array values fall back to the default (run all phases), preserving the prior behavior for callers who didn't ask for selective phases.
+
+### What this means for you
+
+If you've been using `gbrain jobs submit autopilot-cycle --params '{"phases":[...]}'` for triage cycles (e.g. `["lint","backlinks"]` for a fast structural sweep, skipping the slow embed phase), you'll now see those cycles take seconds instead of minutes. The CLI surface didn't change — only the worker's handler now respects the `phases` it was already accepting.
+
+### Itemized changes
+
+#### Fixed
+
+- `autopilot-cycle` minion handler in `src/commands/jobs.ts` now forwards `job.data.phases` to `runCycle()`. Previously the handler accepted the array via `MinionJobInput.params` but discarded it before dispatch.
+- Phase names validated against `ALL_PHASES` from `src/core/cycle.ts`. Filter is exhaustive: array → filtered, non-array → undefined (default), filtered-to-empty → no `phases` key in opts (also default).
+
+#### Tests
+
+- 4 new test cases in `test/handlers.test.ts` under `autopilot-cycle handler — phase passthrough`: valid phases forwarded, invalid names filtered, empty array falls back to all-phases, non-array `phases` value ignored. Pin both the contract and the fallback semantics.
+- `test/cycle-abort.test.ts` regression-guard window widened from 500 → 2000 chars so the source-level `signal: job.signal` check finds the line after the new validation block was added between `worker.register('autopilot-cycle', ...)` and the `runCycle(...)` call. Pure test fix; the handler still propagates the abort signal correctly.
+
+## [0.22.9] - 2026-04-29
+
+**Sync failures now tell you why, not just how many.**
+**`gbrain sync --skip-failed` and `gbrain doctor` group failures by error code, so 2,685 silent SLUG_MISMATCH files don't hide behind a single count.**
+
+Before this release, when sync hit per-file parse errors the only signal was a number:
+
+```
+Sync blocked: 2688 file(s) failed to parse. Fix the YAML frontmatter...
+```
+
+That count is useless when you're staring at 2,688 files and don't know what's wrong. On a real 81K-page brain, 2,685 of those turned out to be `SLUG_MISMATCH` from a posterous import — a single root cause hiding behind a giant number. It took manual `cat ~/.gbrain/sync-failures.jsonl | jq` to figure that out.
+
+After:
+
+```
+Sync blocked: 2688 file(s) failed to parse:
+  SLUG_MISMATCH: 2685
+  YAML_DUPLICATE_KEY: 3
+
+Fix the YAML frontmatter in the files above and re-run, or use 'gbrain sync --skip-failed' to acknowledge and move on.
+
+# gbrain sync --skip-failed
+Acknowledged 2688 failure(s) and advancing past them:
+  SLUG_MISMATCH: 2685
+  YAML_DUPLICATE_KEY: 3
+```
+
+`gbrain doctor` shows the same breakdown for unacknowledged AND historical entries:
+
+```
+[WARN] sync_failures: 2688 unacknowledged sync failure(s) [SLUG_MISMATCH=2685, YAML_DUPLICATE_KEY=3].
+[OK]   sync_failures: 500544 historical sync failure(s), all acknowledged [SLUG_MISMATCH=2685, ...].
+```
+
+The classifier knows the canonical messages from `collectValidationErrors()` in `src/core/markdown.ts` (8 frontmatter codes), Postgres unique-constraint violations (`DB_DUPLICATE_KEY`), statement-timeout errors (`STATEMENT_TIMEOUT`), invalid UTF-8, and YAML duplicates. DB-layer errors check before YAML-layer ones — so a Postgres `duplicate key value violates unique constraint` no longer mislabels as a YAML duplicate. Unrecognized errors fall through to `UNKNOWN`.
+
+### What this means for you
+
+If `gbrain sync` blocks with parse failures, the breakdown tells you what to fix first. SLUG_MISMATCH is one fix-pattern (frontmatter says one slug, path says another); YAML_PARSE is a different one (malformed YAML); STATEMENT_TIMEOUT means a DB timeout, not a parse problem. You stop staring at counts and start fixing root causes.
+
+### For contributors
+
+`acknowledgeSyncFailures()` in `src/core/sync.ts` now returns `{count, summary}` instead of `number`. If you import this directly from `gbrain/sync`, replace `n` with `result.count` and use `result.summary` (an `Array<{code, count}>`) for the new code-grouped breakdown. The function is reachable via the package exports map; this is a deliberate, non-shimmed breaking change. There is a new `formatCodeBreakdown()` helper in the same module that accepts either raw failures or pre-summarized input — use it instead of building breakdown strings inline.
+
+### Itemized changes
+
+#### Added
+
+- `classifyErrorCode(errorMsg)` in `src/core/sync.ts` — best-effort error-code extraction from sync failure messages. Codes: `SLUG_MISMATCH`, `YAML_PARSE`, `YAML_DUPLICATE_KEY`, `MISSING_OPEN`, `MISSING_CLOSE`, `EMPTY_FRONTMATTER`, `NULL_BYTES`, `NESTED_QUOTES`, `DB_DUPLICATE_KEY`, `STATEMENT_TIMEOUT`, `INVALID_UTF8`, `UNKNOWN`.
+- `summarizeFailuresByCode(failures)` — groups failures by code and returns a sorted `Array<{code, count}>`.
+- `formatCodeBreakdown(input)` — renders a multi-line `code: count` string from either raw failures or a pre-computed summary. Single helper, two input shapes.
+- `code?: string` field on the `SyncFailure` JSONL row in `~/.gbrain/sync-failures.jsonl`. Populated at write-time so the classifier runs once per failure, not on every load.
+- `AcknowledgeResult` interface as the new return shape of `acknowledgeSyncFailures()`.
+- 15 new test cases in `test/sync-failures.test.ts`: DB-vs-YAML duplicate-key disambiguation, canonical-message coverage for all 7 frontmatter codes, `acknowledgeSyncFailures()` legacy-entry backfill branch, `formatCodeBreakdown()` dual-input shape.
+
+#### Changed
+
+- `gbrain sync` blocked-message: now lists code breakdown above the fix instructions (both incremental and full-sync paths).
+- `gbrain sync --skip-failed` ack message: now lists what was skipped, grouped by code.
+- `gbrain doctor` `sync_failures` check: warn-and-ok messages both include `[code=count, ...]` breakdown.
+- `recordSyncFailures()` now stores `code` alongside `error` so downstream readers don't re-classify.
+- `acknowledgeSyncFailures()` backfills `code` on legacy rows that predate the field — upgrade-safe for users with existing `~/.gbrain/sync-failures.jsonl`.
+- DB-layer error patterns (`DB_DUPLICATE_KEY`, `STATEMENT_TIMEOUT`) check BEFORE YAML patterns in the classifier, so Postgres errors don't get YAML-labeled.
+- Frontmatter regex patterns rewritten to match canonical messages from `collectValidationErrors()` (`File is empty...`, `No closing --- delimiter found`, `Frontmatter block is empty`) instead of aspirational code-token strings (`missing.*open`) that never appeared in practice.
+
+Closes #500.
+
+## [0.22.8] - 2026-04-28
+
+## **Doctor stops timing out on Supabase. Integrity scan finishes in ~6s, multi-source brains get correct counts.**
+
+If you've been hitting the 60-second `gbrain doctor` timeout on Supabase or any pooled-connection deployment, this fixes it. The integrity check used to call `getPage()` 500 times sequentially through PgBouncer transaction-mode pooling. Each call required a full connection acquire/release cycle, which doctor couldn't finish before CI killed it. The new path batch-loads all 500 pages in a single SQL query, finishing in ~6s.
+
+While shipping the perf fix, codex review caught a correctness regression for multi-source brains: the batch SQL was scanning raw `(source_id, slug)` rows while the sequential path scanned unique slugs. Multi-source brains were getting inflated counts. `SELECT DISTINCT ON (slug)` mirrors the sequential path's `Set<string>` semantics; parity tests against real Postgres pin both paths to the same output.
+
+Plus a Linux CI fix: `gbrain skillpack` lockfile checks were intermittently failing on ext4's sub-millisecond `mtimeMs` timestamps when `Date.now()` returned an integer ms behind the file's recorded mtime. Lock age now clamps to zero.
+
+### The numbers that matter
+
+Measured against the real failure mode on a Supabase PgBouncer deployment that hit the 60s CI timeout pre-fix.
+
+| Behavior | Before v0.22.8 | After v0.22.8 |
+|---|---|---|
+| `gbrain doctor` wall-clock (Postgres + PgBouncer) | 60s+ timeout (killed) | ~6s |
+| `integrity_sample` query round-trips | ~500 (sequential `getPage`) | 1 (`SELECT DISTINCT ON`) |
+| Multi-source brain scan accuracy | Overcounted by `source_id` | Exact per unique slug |
+
+### What this means for Supabase deployments
+
+If you've been avoiding `gbrain doctor` because it timed out, run it again. If you maintain a multi-source brain (imported pages from another gbrain deployment under a non-default `source_id`), the scan now treats each slug once instead of once-per-source — your output is exact, not inflated. Single-source users see no behavior change; PGLite users were never affected (the batch path is Postgres-only).
+
+## To take advantage of v0.22.8
+
+`gbrain upgrade` should do this automatically. If it didn't, or if `gbrain doctor` warns about anything afterwards:
+
+1. **Run the upgrade:**
+   ```bash
+   gbrain upgrade
+   ```
+2. **Verify doctor finishes cleanly (especially relevant if you hit timeouts before):**
+   ```bash
+   gbrain doctor
+   ```
+   On Postgres + PgBouncer deployments, you should see `integrity_sample` finish in ~6s instead of timing out at 60s.
+3. **If `doctor` still times out or output looks wrong,** please file an issue:
+   https://github.com/garrytan/gbrain/issues with:
+   - output of `gbrain doctor` (full)
+   - which engine (Postgres vs PGLite)
+   - whether you use multi-source brains
+
+### Itemized changes
+
+#### Performance
+- `gbrain doctor` integrity sample now batch-loads via a single SQL query on Postgres deployments (60s+ timeout → ~6s wall-clock, 500 round-trips → 1).
+- Batch path explicitly gated to Postgres via `engine.kind` so PGLite never attempts it (clean fallback signal).
+
+#### Correctness
+- `scanIntegrity` batch path uses `SELECT DISTINCT ON (slug)` to scope by unique slug, matching `engine.getAllSlugs()`'s `Set<string>` semantics. Multi-source brains (UNIQUE(source_id, slug) since v0.18.0) now get correct counts instead of one-scan-per-source-row.
+- `IntegrityScanResult.pagesScanned` now reflects unique slugs scanned, not raw row count. Single-source brains: unchanged. Multi-source brains: counts now match expected distinct-page semantics.
+- Batch-path fallback narrowed: real Postgres errors (deadlock, connection drop, SQL bug) surface via `GBRAIN_DEBUG=1` instead of being silently swallowed.
+
+#### Tests
+- New `test/e2e/integrity-batch.test.ts` — four parity cases (dedup, hits, validate, topPages) asserting batch ≡ sequential against real Postgres. Pinning the multi-source dedup case requires a raw-SQL fixture for the alt-source row since `engine.putPage` doesn't take a `source_id`.
+
+#### Infrastructure
+- `src/core/skillpack/installer.ts` — clamp negative lock-age to 0, fixing intermittent Linux ext4 CI flakes from sub-millisecond `mtimeMs` precision (Date.now is integer ms; mtime can be ~0.3ms ahead). New regression test in `test/skillpack-install.test.ts` deterministically reproduces via `utimesSync`.
+- `CLAUDE.md` test inventory updated for the new test files.
+
+## [0.22.7] - 2026-04-28
+
+## **Built-in HTTP transport with bearer auth for remote MCP.**
+## **Postgres-backed tokens, default-deny CORS, two-bucket rate limit, body cap, per-request audit.**
+
+v0.22.7 ships `gbrain serve --http`: a built-in HTTP transport for remote MCP, authenticating via the existing `access_tokens` table that `gbrain auth create/list/revoke` already manages. Bearer-only, no OAuth surface, no registration endpoint, no self-service tokens. SECURITY.md is the canonical reference for the hardening posture and recommended deployment.
+
+The hardening lives inside the transport, not in the doc:
+
+| Layer | Default | Configurable via |
+|---|---|---|
+| CORS | default-deny (no `Access-Control-Allow-Origin`) | `GBRAIN_HTTP_CORS_ORIGIN=a.com,b.com` |
+| Pre-auth IP rate limit | 30 req / 60s | `GBRAIN_HTTP_RATE_LIMIT_IP` |
+| Post-auth token rate limit | 60 req / 60s | `GBRAIN_HTTP_RATE_LIMIT_TOKEN` |
+| Body cap | 1 MiB, stream-counted | `GBRAIN_HTTP_MAX_BODY_BYTES` |
+| `last_used_at` debounce | once per token per 60s | (SQL-level WHERE clause, race-tolerant) |
+| Per-request audit | `mcp_request_log` row per `/mcp` | (existing schema, since v4) |
+| Reverse-proxy trust | off | `GBRAIN_HTTP_TRUST_PROXY=1` to honor X-Forwarded-For |
+
+The IP rate-limit fires **before** the auth lookup so the limit caps load on the auth path itself, not just response codes. The token-id rate limit fires after auth so a runaway authenticated client gets throttled at the right principal. Both buckets live in a bounded LRU map (default 10K keys, TTL prune at 2× window) so unique-key growth can't drift into memory pressure.
+
+### What changed for users
+
+You can now expose GBrain remotely with the built-in transport:
+
+```bash
+gbrain auth create my-laptop                    # tokens managed via the existing CLI
+gbrain serve --http --port 8787                  # Postgres-only; PGLite users see a clear fail-fast
+ngrok http 8787 --url your-brain.ngrok.app       # any tunnel works
+```
+
+Then point Claude Desktop, claude.ai/code, or any MCP client at `http://your-tunnel/mcp` with `Authorization: Bearer <token>`. CORS, rate limits, and body caps are on by default. `gbrain auth` is now wired into the main CLI, so it works from the compiled binary the same as `gbrain doctor` or `gbrain serve`.
+
+### For contributors
+
+- `src/mcp/dispatch.ts` (new) — shared `dispatchToolCall(engine, name, params, opts)` consumed by both stdio (`server.ts`) and HTTP (`http-transport.ts`). One source of truth for `validateParams`, `OperationContext` construction, and handler invocation, so the two transports can't drift apart.
+- `src/mcp/rate-limit.ts` (new) — bounded-LRU token-bucket. Tracks `lastTouchedMs` separately from `lastRefillMs` so an exhausted key can't be reset by hammering past the TTL.
+- `src/mcp/http-transport.ts` — built on the new dispatch + rate-limit modules. `application/json` response shape (gbrain MCP tools are synchronous; the Streamable HTTP transport spec allows JSON for non-streaming responses).
+- `src/cli.ts` + `src/commands/auth.ts` — `auth` is now a wired CLI subcommand. Direct-script usage (`bun run src/commands/auth.ts ...`) still works for environments without a compiled binary.
+- 23 unit cases in `test/http-transport.test.ts`, 8 E2E cases in `test/e2e/http-transport.test.ts`. Unit covers the full dispatch round-trip with a real operation; E2E covers `last_used_at` debounce against real Postgres semantics.
+
+### Known limits
+
+- `gbrain serve --http` is **Postgres-only**. PGLite has no `access_tokens` or `mcp_request_log` table by design (`src/core/pglite-schema.ts:5-6`). Local agents continue to use stdio (`gbrain serve`).
+- Behind a tunnel (ngrok, Tailscale Funnel, Cloudflare Tunnel), all requests share one egress IP. The pre-auth IP bucket becomes effectively shared by all clients on that tunnel; the token-id bucket is the load-bearing limiter for tunnel deployments. Documented in SECURITY.md.
+
+### Itemized changes
+
+- New: `gbrain serve --http [--port N]` ships the built-in HTTP transport
+- New: `gbrain auth create/list/revoke/test` wired into the main CLI (was a standalone script)
+- New: SECURITY.md documents the disclosure path, the recommended remote-MCP setup, and the full hardening reference
+- New: `src/mcp/dispatch.ts` — shared dispatch path for stdio + HTTP
+- New: `src/mcp/rate-limit.ts` — bounded-LRU token-bucket limiter
+- Hardening: CORS default-deny, two-bucket rate limit (per-IP pre-auth + per-token post-auth), 1 MiB body cap with stream-counted enforcement, `mcp_request_log` per-request audit, `last_used_at` SQL-level debounce
+- Tests: 23 unit + 8 E2E covering auth, dispatch, CORS, body cap, rate limit, and audit
+- Docs: SECURITY.md, DEPLOY.md, and per-client setup guides updated to recommend `--http` and document the env vars
+
+## To take advantage of v0.22.7
+
+`gbrain upgrade` should do this automatically. If it didn't, or if you want to expose your brain over HTTP:
+
+1. **Confirm migrations are at v4 or higher** (the `access_tokens` + `mcp_request_log` tables were added in migration v4):
+   ```bash
+   gbrain doctor              # schema_version check should pass
+   gbrain apply-migrations --yes  # if not, run this
+   ```
+2. **Create a token for each remote client:**
+   ```bash
+   gbrain auth create my-laptop     # prints the token once — copy it
+   ```
+3. **Start the HTTP server:**
+   ```bash
+   gbrain serve --http --port 8787
+   ```
+4. **(Optional) configure CORS allowlist if a browser client will hit it:**
+   ```bash
+   GBRAIN_HTTP_CORS_ORIGIN=https://claude.ai gbrain serve --http --port 8787
+   ```
+5. **(Optional) audit who's hitting your brain:**
+   ```bash
+   psql $DATABASE_URL -c "SELECT created_at, token_name, operation, status, latency_ms
+                          FROM mcp_request_log ORDER BY created_at DESC LIMIT 50"
+   ```
+6. **If `gbrain serve --http` exits with "Postgres engine required":** PGLite is local-only by design. Either keep using stdio (`gbrain serve`) for local agents, or migrate to Postgres (`gbrain migrate --to supabase`).
+
+If anything breaks: `gbrain doctor`, `~/.gbrain/upgrade-errors.jsonl` (if present), and please file an issue at https://github.com/garrytan/gbrain/issues with both.
+
+## [0.22.6.1] - 2026-04-26
+
+**Old brains can upgrade again.**
+**Two-year, ten-issue wedge cycle ends. Pre-v0.13/v0.18/v0.19 brains all upgrade clean.**
+
+If you've been pinned to an older gbrain because `gbrain upgrade` wedges your brain
+with `column "source_id" does not exist` or `column "link_source" does not exist`,
+v0.22.6.1 unblocks you. The fix lives in `initSchema()` itself, where it should
+have lived all along.
+
+The bug class is structural: gbrain ships an "embedded latest schema" SQL blob
+that runs before numbered migrations on every connect. The blob references
+columns that newer migrations introduce. On any brain older than the migration
+that adds those columns, the blob crashes before the migration can run. This
+incident family hit users 10+ times across 6 schema versions over 2 years
+(issues #239, #243, #266, #357, #366, #374, #375, #378, #395, #396).
+
+The fix is a narrow pre-schema bootstrap. `initSchema()` now probes for the
+specific forward-referenced state the schema blob needs (`pages.source_id`,
+`links.link_source`, `links.origin_page_id`, `content_chunks.symbol_name`,
+`content_chunks.language`, plus the `sources` FK target table) and adds only
+that state if missing. Then SCHEMA_SQL replays cleanly. Then the normal
+migration chain runs as usual. Fresh installs and modern brains both no-op.
+
+A test guard prevents this incident family from recurring. Every future
+migration that adds a column-with-index to PGLITE_SCHEMA_SQL must extend the
+bootstrap; the CI guard fails loudly if not. The pattern that broke gbrain ten
+times in two years is now structurally prevented.
+
+Also includes the v24 PGLite RLS fix from #395 (community PR by @jdcastro2):
+`rls_backfill_missing_tables` now no-ops on PGLite via `sqlFor.pglite: ''`,
+since PGLite has no RLS engine and is single-tenant by definition.
+
+### The numbers that matter
+
+| Metric | v0.22.0 | v0.22.6.1 | Δ |
+|---|---|---|---|
+| Pre-v0.13 brain upgrades cleanly | wedges on `link_source` | passes | ✓ |
+| Pre-v0.18 brain upgrades cleanly | wedges on `source_id` | passes | ✓ |
+| Pre-v0.21 brain upgrades cleanly | wedges on `symbol_name` | passes | ✓ |
+| v24 RLS migration on PGLite | wedges (table doesn't exist) | no-op | ✓ |
+| Issues closed | — | #366, #375, #378, #395, #396 | 5 |
+| Issue families resolved | — | wedge-cycle | the whole class |
+
+### What this means for you
+
+If you've been on v0.13.x, v0.14.x, v0.17.x, v0.18.x, v0.19.x, v0.20.x, or v0.22.0 and
+your `gbrain upgrade` failed, run it again. It should walk to v0.22.6.1 cleanly.
+If you wedged on the v24 RLS migration on a PGLite brain, the same thing.
+
+If you're on a fresh install or already on v0.22.0, this patch is invisible.
+The bootstrap probe runs once per connect, sees nothing to do, and returns.
+
+### Itemized changes
+
+#### Fixed
+- `gbrain upgrade` no longer wedges on pre-v0.18 brains that lack `pages.source_id`. The schema blob's `CREATE INDEX idx_pages_source_id` previously crashed before migration v21 could add the column. Closes #366, #375, #378, #396.
+- `gbrain upgrade` no longer wedges on pre-v0.13 brains that lack `links.link_source` or `links.origin_page_id`. The schema blob's `CREATE INDEX idx_links_source/origin` previously crashed before migration v11 could add the columns. Closes #266, #357.
+- `gbrain upgrade` no longer wedges on pre-v0.19 brains that lack `content_chunks.symbol_name` or `content_chunks.language`. The schema blob's partial indexes previously crashed before migration v26 could add the columns.
+- Migration v24 (`rls_backfill_missing_tables`) no-ops on PGLite via `sqlFor.pglite: ''`. PGLite has no RLS engine and is single-tenant. The migration previously tried to ALTER subagent tables that don't exist in pglite-schema.ts. Closes #395. Contributed by @jdcastro2.
+
+#### Changed
+- `PGLiteEngine.initSchema()` and `PostgresEngine.initSchema()` now call a new private `applyForwardReferenceBootstrap()` before running the embedded schema blob. The bootstrap probes for missing forward-referenced state and adds only what's needed. No-op on fresh installs and modern brains.
+
+#### For contributors
+- New CI guard `test/schema-bootstrap-coverage.test.ts` enforces that `applyForwardReferenceBootstrap` covers every forward reference in PGLITE_SCHEMA_SQL. When you add a new column-with-index in the schema blob, extend `REQUIRED_BOOTSTRAP_COVERAGE` and the bootstrap function. The test fails loudly if you skip step one.
+- New `test/bootstrap.test.ts` covers the bootstrap contract: no-op on fresh install, idempotent, no-op on modern brain, full path pre-v0.18, fresh-install regression, pre-v0.13 links shape.
+- New `test/e2e/postgres-bootstrap.test.ts` exercises `PostgresEngine.initSchema()` directly (not the standalone `db.initSchema` from `src/core/db.ts`, which only runs SCHEMA_SQL and would have produced false-positive coverage). Codex caught this E2E shape gap during plan review.
+- Wave PRs incorporated with attribution: @vinsew (#398), @jdcastro2 (#399), @schnubb-web (#402). The narrow-bootstrap shape supersedes #402's broader "run all migrations early" approach, which would have crashed on v24 trying to alter tables that the schema blob hadn't created yet (codex finding during plan review).
+
+## To take advantage of v0.22.6.1
+
+`gbrain upgrade` should do this automatically. If you're currently wedged on a
+prior version's upgrade attempt:
+
+1. **Run the upgrade:**
+   ```bash
+   gbrain upgrade
+   ```
+2. **Verify the outcome:**
+   ```bash
+   gbrain doctor
+   ```
+   Expected: `schema_version: Version 29 (latest: 29)` clean, no
+   `column "..." does not exist` errors, no wedged migration ledger.
+
+3. **If wedged after upgrade,** run the migration runner directly:
+   ```bash
+   gbrain apply-migrations --yes
+   ```
+
+4. **If any step still fails,** please file an issue:
+   https://github.com/garrytan/gbrain/issues with:
+   - output of `gbrain doctor`
+   - your prior gbrain version (`gbrain --version`)
+   - which step broke
+
 ## [0.22.6] - 2026-04-28
 
 ### Schema verification after migrations

CLAUDE.md

@@ -25,15 +25,19 @@ strict behavior when unset.
 - `src/core/operations.ts` — Contract-first operation definitions (the foundation). Also exports upload validators: `validateUploadPath`, `validatePageSlug`, `validateFilename`. `OperationContext.remote` flags untrusted callers.
 - `src/core/engine.ts` — Pluggable engine interface (BrainEngine). `clampSearchLimit(limit, default, cap)` takes an explicit cap so per-operation caps can be tighter than `MAX_SEARCH_LIMIT`. Exports `LinkBatchInput` / `TimelineBatchInput` for the v0.12.1 bulk-insert API (`addLinksBatch` / `addTimelineEntriesBatch`). As of v0.13.1, `BrainEngine` has a `readonly kind: 'postgres' | 'pglite'` discriminator so migrations (`src/core/migrate.ts`) and other consumers can branch on engine without `instanceof` + dynamic imports.
 - `src/core/engine-factory.ts` — Engine factory with dynamic imports (`'pglite'` | `'postgres'`)
-- `src/core/pglite-engine.ts` — PGLite (embedded Postgres 17.5 via WASM) implementation, all 40 BrainEngine methods. `addLinksBatch` / `addTimelineEntriesBatch` use multi-row `unnest()` with manual `$N` placeholders. As of v0.13.1, `connect()` wraps `PGlite.create()` in a try/catch that emits an actionable error naming the macOS 26.3 WASM bug (#223) and pointing at `gbrain doctor`; the lock is released on failure so the next process can retry cleanly. v0.22.0: `searchKeyword` and `searchKeywordChunks` multiply `ts_rank` by the source-factor CASE expression at the chunk-grain level; `searchVector` becomes a two-stage CTE — inner CTE keeps `ORDER BY cc.embedding <=> vec` so HNSW stays usable, outer SELECT re-ranks by `raw_score * source_factor`. Inner LIMIT scales with offset to preserve pagination contract.
+- `src/core/pglite-engine.ts` — PGLite (embedded Postgres 17.5 via WASM) implementation, all 40 BrainEngine methods. `addLinksBatch` / `addTimelineEntriesBatch` use multi-row `unnest()` with manual `$N` placeholders. As of v0.13.1, `connect()` wraps `PGlite.create()` in a try/catch that emits an actionable error naming the macOS 26.3 WASM bug (#223) and pointing at `gbrain doctor`; the lock is released on failure so the next process can retry cleanly. v0.22.0: `searchKeyword` and `searchKeywordChunks` multiply `ts_rank` by the source-factor CASE expression at the chunk-grain level; `searchVector` becomes a two-stage CTE — inner CTE keeps `ORDER BY cc.embedding <=> vec` so HNSW stays usable, outer SELECT re-ranks by `raw_score * source_factor`. Inner LIMIT scales with offset to preserve pagination contract. As of v0.22.6.1, `initSchema()` calls `applyForwardReferenceBootstrap()` BEFORE replaying SCHEMA_SQL — probes for the specific forward-referenced state the embedded schema blob needs (`pages.source_id`, `links.link_source`, `links.origin_page_id`, `content_chunks.symbol_name`, `content_chunks.language`, `sources` FK target table) and adds only what's missing. Closes the upgrade-wedge bug class that bit users 10+ times across 6 schema versions over 2 years (#239/#243/#266/#357/#366/#374/#375/#378/#395/#396). No-op on fresh installs and modern brains.
 - `src/core/pglite-schema.ts` — PGLite-specific DDL (pgvector, pg_trgm, triggers)
-- `src/core/postgres-engine.ts` — Postgres + pgvector implementation (Supabase / self-hosted). `addLinksBatch` / `addTimelineEntriesBatch` use `INSERT ... SELECT FROM unnest($1::text[], ...) JOIN pages ON CONFLICT DO NOTHING RETURNING 1` — 4-5 array params regardless of batch size, sidesteps the 65535-parameter cap. As of v0.12.3, `searchKeyword` / `searchVector` scope `statement_timeout` via `sql.begin` + `SET LOCAL` so the GUC dies with the transaction instead of leaking across the pooled postgres.js connection (contributed by @garagon). `getEmbeddingsByChunkIds` uses `tryParseEmbedding` so one corrupt row skips+warns instead of killing the query. v0.22.0: `searchKeyword`, `searchKeywordChunks`, and `searchVector` apply source-aware ranking by inlining the source-factor CASE and `NOT (col LIKE …)` hard-exclude clause from `src/core/search/sql-ranking.ts`. `searchVector` switches to a two-stage CTE (HNSW-safe inner ORDER BY, source-boost re-rank in the outer SELECT) and carries `p.source_id` through inner→outer for v0.18 multi-source callers. v0.22.1 (#406): `_savedConfig` retains the connect config; `reconnect()` tears down + recreates the pool from saved config (called by supervisor watchdog after 3 consecutive health-check failures). `executeRaw` is a single-statement passthrough — no per-call retry (D3 dropped that as unsound for non-idempotent statements; recovery is supervisor-driven). v0.22.1 (#363, contributed by @orendi84): `connect()` applies `resolveSessionTimeouts()` from `db.ts` as connection-time startup parameters (`statement_timeout`, `idle_in_transaction_session_timeout`) so orphan pgbouncer backends can't hold locks for hours. v0.22.1 (#409, contributed by @atrevino47): `countStaleChunks()` + `listStaleChunks()` server-side-filter on `embedding IS NULL` for `embed --stale`, eliminating ~76 MB/call client-side pull on a fully-embedded brain; `upsertChunks()` resets both `embedding` AND `embedded_at` to NULL when chunk_text changes without a new embedding (consistency).
+- `src/core/postgres-engine.ts` — Postgres + pgvector implementation (Supabase / self-hosted). `addLinksBatch` / `addTimelineEntriesBatch` use `INSERT ... SELECT FROM unnest($1::text[], ...) JOIN pages ON CONFLICT DO NOTHING RETURNING 1` — 4-5 array params regardless of batch size, sidesteps the 65535-parameter cap. As of v0.12.3, `searchKeyword` / `searchVector` scope `statement_timeout` via `sql.begin` + `SET LOCAL` so the GUC dies with the transaction instead of leaking across the pooled postgres.js connection (contributed by @garagon). `getEmbeddingsByChunkIds` uses `tryParseEmbedding` so one corrupt row skips+warns instead of killing the query. v0.22.0: `searchKeyword`, `searchKeywordChunks`, and `searchVector` apply source-aware ranking by inlining the source-factor CASE and `NOT (col LIKE …)` hard-exclude clause from `src/core/search/sql-ranking.ts`. `searchVector` switches to a two-stage CTE (HNSW-safe inner ORDER BY, source-boost re-rank in the outer SELECT) and carries `p.source_id` through inner→outer for v0.18 multi-source callers. v0.22.1 (#406): `_savedConfig` retains the connect config; `reconnect()` tears down + recreates the pool from saved config (called by supervisor watchdog after 3 consecutive health-check failures). `executeRaw` is a single-statement passthrough — no per-call retry (D3 dropped that as unsound for non-idempotent statements; recovery is supervisor-driven). v0.22.1 (#363, contributed by @orendi84): `connect()` applies `resolveSessionTimeouts()` from `db.ts` as connection-time startup parameters (`statement_timeout`, `idle_in_transaction_session_timeout`) so orphan pgbouncer backends can't hold locks for hours. v0.22.1 (#409, contributed by @atrevino47): `countStaleChunks()` + `listStaleChunks()` server-side-filter on `embedding IS NULL` for `embed --stale`, eliminating ~76 MB/call client-side pull on a fully-embedded brain; `upsertChunks()` resets both `embedding` AND `embedded_at` to NULL when chunk_text changes without a new embedding (consistency). As of v0.22.6.1, `initSchema()` calls `applyForwardReferenceBootstrap()` BEFORE replaying SCHEMA_SQL on the same forward-reference probe set as the PGLite engine, so old Postgres brains pinned at v0.13/v0.18/v0.19 walk forward cleanly instead of wedging on `column "..." does not exist`.
 - `src/core/utils.ts` — Shared SQL utilities extracted from postgres-engine.ts. Exports `parseEmbedding(value)` (throws on unknown input, used by migration + ingest paths where data integrity matters) and as of v0.12.3 `tryParseEmbedding(value)` (returns `null` + warns once per process, used by search/rescore paths where availability matters more than strictness).
 - `src/core/db.ts` — Connection management, schema initialization. v0.22.1 (#363, contributed by @orendi84): `resolveSessionTimeouts()` returns `statement_timeout` + `idle_in_transaction_session_timeout` (defaults: 5min each, env-overridable via `GBRAIN_STATEMENT_TIMEOUT` / `GBRAIN_IDLE_TX_TIMEOUT` / `GBRAIN_CLIENT_CHECK_INTERVAL`). Both `connect()` (module singleton) and `PostgresEngine.connect()` (worker pool) consume the result via postgres.js's `connection` option, sending GUCs as startup parameters that survive PgBouncer transaction mode (unlike the prior `setSessionDefaults` post-pool SET, kept as a back-compat no-op shim).
 - `src/commands/migrate-engine.ts` — Bidirectional engine migration (`gbrain migrate --to supabase/pglite`)
 - `src/core/import-file.ts` — importFromFile + importFromContent (chunk + embed + tags)
-- `src/core/sync.ts` — Pure sync functions (manifest parsing, filtering, slug conversion)
+- `src/core/sync.ts` — Pure sync functions (manifest parsing, filtering, slug conversion). v0.22.12 (#500, foundation by @wintermute via #501): `classifyErrorCode(errorMsg)` regex-based classifier with 12 codes (`SLUG_MISMATCH`, `YAML_PARSE`, `YAML_DUPLICATE_KEY`, `MISSING_OPEN`, `MISSING_CLOSE`, `NESTED_QUOTES`, `EMPTY_FRONTMATTER`, `NULL_BYTES`, `INVALID_UTF8`, `STATEMENT_TIMEOUT`, `FILE_TOO_LARGE`, `SYMLINK_NOT_ALLOWED`) plus `UNKNOWN` fallback. `summarizeFailuresByCode(failures)` returns sorted `[{code, count}]`. `code?` optional field on `SyncFailure`; backfilled at ack time on pre-v0.22.12 entries. `acknowledgeSyncFailures()` returns `AcknowledgeResult { count, summary }`. Three regexes (`MISSING_OPEN`, `MISSING_CLOSE`, `EMPTY_FRONTMATTER`) broadened to match actual `markdown.ts:159-244` validator message strings, not just the literal code-name prefix. `FILE_TOO_LARGE` covers all three production size sites in `import-file.ts:199, 352, 401`; `SYMLINK_NOT_ALLOWED` covers the rejection at `:347`. Closes the silent-skip pattern that motivated #500.
 - `src/core/storage.ts` — Pluggable storage interface (S3, Supabase Storage, local)
+- `src/core/storage-config.ts` (v0.22.11) — Storage tiering: `loadStorageConfig` reads `gbrain.yml`, normalizes deprecated keys (`git_tracked` / `supabase_only`) to canonical (`db_tracked` / `db_only`) with once-per-process deprecation warning, and runs `normalizeAndValidateStorageConfig` (auto-fixes missing trailing `/`, throws `StorageConfigError` on tier overlap). Path-segment matcher: `media/x/` does NOT match `media/xerox/foo`. Replaces gray-matter (broken on delimiter-less YAML) with a dedicated parser for the `gbrain.yml` shape.
+- `src/core/disk-walk.ts` (v0.22.11) — `walkBrainRepo(repoPath)` returns `Map<slug, {size, mtimeMs}>` from one recursive `readdirSync`. Skips dot-dirs, `node_modules`, non-`.md` files. Used by `gbrain storage status` to replace per-page `existsSync + statSync` (~400K syscalls on 200K-page brains → tens).
+- `src/commands/storage.ts` (v0.22.11) — `gbrain storage status [--repo P] [--json]`. Split into pure data (`getStorageStatus`) + JSON formatter + human formatter (ASCII-only per D10) matching the `orphans.ts` pattern. `PageCountsByTier` and `DiskUsageByTier` are distinct nominal types so swaps fail at compile time.
+- `gbrain.yml` (brain repo root, v0.22.11) — Optional storage tiering config. Top-level `storage:` section with `db_tracked:` and `db_only:` array-valued keys. `gbrain sync` auto-manages `.gitignore` for `db_only` paths on successful sync (skips on dry-run, blocked-by-failures, submodule context, or `GBRAIN_NO_GITIGNORE=1`). `gbrain export --restore-only [--repo P] [--type T] [--slug-prefix S]` repopulates missing `db_only` files from the database.
 - `src/core/supabase-admin.ts` — Supabase admin API (project discovery, pgvector check)
 - `src/core/file-resolver.ts` — File resolution with fallback chain (local -> .redirect.yaml -> .redirect -> .supabase)
 - `src/core/chunkers/` — 3-tier chunking (recursive, semantic, LLM-guided). v0.19.0 adds `code.ts` — tree-sitter-based semantic chunker for 29 languages with embedded-asset WASMs (`src/assets/wasm/`), `@dqbd/tiktoken` cl100k_base tokenizer, small-sibling merging. `CHUNKER_VERSION` constant folded into `importCodeFile`'s `content_hash` so chunker shape changes force clean re-chunks across releases.
@@ -88,19 +92,26 @@ strict behavior when unset.
 - `src/core/minions/attachments.ts` — Attachment validation (path traversal, null byte, oversize, base64, duplicate detection)
 - `src/commands/agent.ts` (v0.16) — `gbrain agent run <prompt> [flags]` CLI. Submits `subagent` (or N children + 1 aggregator) under `{allowProtectedSubmit: true}`. Single-entry `--fanout-manifest` short-circuits. Children get `on_child_fail: 'continue'` + `max_stalled: 3`. `--follow` is the default on TTY; streams logs + polls `waitForCompletion` in parallel. Ctrl-C detaches, does not cancel.
 - `src/commands/agent-logs.ts` (v0.16) — `gbrain agent logs <job> [--follow] [--since]`. Merges JSONL heartbeat audit + `subagent_messages` into a chronological timeline. `parseSince` accepts ISO-8601 or relative (`5m`, `1h`, `2d`). Transcript tail renders only for terminal jobs.
-- `src/commands/jobs.ts` — `gbrain jobs` CLI subcommands + `gbrain jobs work` daemon. v0.13.1 surfaces the full `MinionJobInput` retry/backoff/timeout/idempotency surface as first-class CLI flags on `jobs submit`: `--max-stalled`, `--backoff-type fixed|exponential`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key`. `jobs smoke --sigkill-rescue` is the opt-in regression guard for #219. v0.16 wires `registerBuiltinHandlers` to always register `subagent` + `subagent_aggregator` (no env flag — `ANTHROPIC_API_KEY` is the natural cost gate, trust is via `PROTECTED_JOB_NAMES`) and loads `GBRAIN_PLUGIN_PATH` plugins at worker startup with a loud startup-line per plugin. `shell` handler still gated by `GBRAIN_ALLOW_SHELL_JOBS=1` (RCE surface, separate concern).
+- `src/commands/jobs.ts` — `gbrain jobs` CLI subcommands + `gbrain jobs work` daemon. v0.13.1 surfaces the full `MinionJobInput` retry/backoff/timeout/idempotency surface as first-class CLI flags on `jobs submit`: `--max-stalled`, `--backoff-type fixed|exponential`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key`. `jobs smoke --sigkill-rescue` is the opt-in regression guard for #219. v0.16 wires `registerBuiltinHandlers` to always register `subagent` + `subagent_aggregator` (no env flag — `ANTHROPIC_API_KEY` is the natural cost gate, trust is via `PROTECTED_JOB_NAMES`) and loads `GBRAIN_PLUGIN_PATH` plugins at worker startup with a loud startup-line per plugin. `shell` handler still gated by `GBRAIN_ALLOW_SHELL_JOBS=1` (RCE surface, separate concern). v0.22.10 (#521): the `autopilot-cycle` handler now forwards `job.data.phases` to `runCycle` (was previously discarded — caller-supplied phase selection silently became a full cycle). Phases are validated against `ALL_PHASES` from `src/core/cycle.ts`; invalid names are filtered out and an empty/missing array falls back to the default 6-phase cycle. v0.22.13 (PR #490 CODEX-1+CODEX-4): `sync` handler now resolves `sourceId` at entry by looking up `sources.local_path` (mirrors `cycle.ts:480`'s autopilot fix from PR #475) so multi-source brains read the per-source `last_commit` anchor instead of the global config key. Concurrency routed through the shared `autoConcurrency()` policy in `src/core/sync-concurrency.ts` instead of the prior hardcoded `4`; PGLite stays serial. `noEmbed` default is `true` (embed is a separate job — submit `gbrain embed --stale` after sync, or rely on the autopilot cycle's embed phase).
 - `src/commands/features.ts` — `gbrain features --json --auto-fix`: usage scan + feature adoption salesman
 - `src/commands/autopilot.ts` — `gbrain autopilot --install`: self-maintaining brain daemon (sync+extract+embed)
-- `src/mcp/server.ts` — MCP stdio server (generated from operations)
-- `src/commands/auth.ts` — Standalone token management (create/list/revoke/test)
+- `src/mcp/server.ts` — MCP stdio server (generated from operations). v0.22.7: tool-call handler delegates to `dispatchToolCall` from `src/mcp/dispatch.ts` so stdio + HTTP transports share one validation, context-build, and error-format path.
+- `src/mcp/dispatch.ts` (v0.22.7) — Shared tool-call dispatch consumed by both stdio (`server.ts`) and HTTP (`http-transport.ts`). Exports `dispatchToolCall(engine, name, params, opts)`, `buildOperationContext(engine, params, opts)`, and `validateParams(op, params)`. Single source of truth for `(ctx, params)` handler arg order and the 5-field `OperationContext` shape (engine + config + logger + dryRun + remote). Defaults to `remote: true` (untrusted); local CLI callers pass `remote: false`. Closed F1 (reversed handler args) + F2 (incomplete OperationContext) + F3 (no param validation) drift bugs in the original v0.22.5 HTTP transport.
+- `src/mcp/rate-limit.ts` (v0.22.7) — Bounded-LRU token-bucket limiter for `gbrain serve --http`. `buildDefaultLimiters()` returns the two-bucket pipeline used by http-transport: pre-auth IP (default 30/60s, fires BEFORE the DB lookup so brute-force load against `access_tokens` is actually capped) + post-auth token-id (default 60/60s). Tracks `lastTouchedMs` separately from `lastRefillMs` so an exhausted key can't be reset by hammering past the TTL. LRU cap (default 10K keys) bounds memory under attacker-controlled key growth; TTL prune at 2× window evicts abandoned buckets.
+- `src/mcp/http-transport.ts` (v0.22.7, rewrite) — `gbrain serve --http` HTTP transport. Postgres-only — fails fast at startup on PGLite (the `access_tokens` table only exists on Postgres). Bearer auth against SHA-256 hashes in `access_tokens`. CORS default-deny via `GBRAIN_HTTP_CORS_ORIGIN` allowlist. Body cap stream-counted (1 MiB default via `GBRAIN_HTTP_MAX_BODY_BYTES`) so chunked transfers without Content-Length still hit the cap. `last_used_at` SQL-level debounce (one UPDATE per token per 60s). Per-request audit row in `mcp_request_log` with token_name + operation + status + latency. Optional `GBRAIN_HTTP_TRUST_PROXY=1` honors `X-Forwarded-For` — only safe when bound to a private interface AND the proxy strips client-supplied XFF (otherwise enables IP spoofing past the pre-auth rate limit). `/health` does `SELECT 1` against Postgres and returns 503 + `status:unhealthy` when the DB is unreachable so orchestration doesn't see green pods while clients get misleading 401s. Replaces the standalone OAuth wrapper that was vulnerable to unauthenticated client registration.
+- `src/commands/auth.ts` — Token management for the HTTP transport. `gbrain auth create/list/revoke/test`. As of v0.22.7 wired into the main CLI (`src/cli.ts`); also runs standalone via `bun run src/commands/auth.ts ...` for environments without a compiled binary. Tokens stored as SHA-256 hashes in `access_tokens` (Postgres-only).
 - `src/commands/upgrade.ts` — Self-update CLI. `runPostUpgrade()` enumerates migrations from the TS registry (src/commands/migrations/index.ts) and tail-calls `runApplyMigrations(['--yes', '--non-interactive'])` so the mechanical side of every outstanding migration runs unconditionally.
 - `src/commands/migrations/` — TS migration registry (compiled into the binary; no filesystem walk of `skills/migrations/*.md` needed at runtime). `index.ts` lists migrations in semver order. `v0_11_0.ts` = Minions adoption orchestrator (8 phases). `v0_12_0.ts` = Knowledge Graph auto-wire orchestrator (5 phases: schema → config check → backfill links → backfill timeline → verify). `phaseASchema` has a 600s timeout (bumped from 60s in v0.12.1 for duplicate-heavy brains). `v0_12_2.ts` = JSONB double-encode repair orchestrator (4 phases: schema → repair-jsonb → verify → record). `v0_14_0.ts` = shell-jobs + autopilot cooperative (2 phases: schema ALTER minion_jobs.max_stalled SET DEFAULT 3 — superseded by v0.14.3's schema-level DEFAULT 5 + UPDATE backfill; pending-host-work ping for skills/migrations/v0.14.0.md). All orchestrators are idempotent and resumable from `partial` status. As of v0.14.2 (Bug 3), the RUNNER owns all ledger writes — orchestrators return `OrchestratorResult` and `apply-migrations.ts` persists a canonical `{version, status, phases}` shape after return. Orchestrators no longer call `appendCompletedMigration` directly. `statusForVersion` prefers `complete` over `partial` (never regresses). 3 consecutive partials → wedged → `--force-retry <version>` writes a `'retry'` reset marker. v0.14.3 (fix wave) ships schema-only migrations v14 (`pages_updated_at_index`) + v15 (`minion_jobs_max_stalled_default_5` with UPDATE backfill) via the `MIGRATIONS` array in `src/core/migrate.ts` — no orchestrator phases needed.
 - `src/commands/repair-jsonb.ts` — `gbrain repair-jsonb [--dry-run] [--json]`: rewrites `jsonb_typeof='string'` rows in place across 5 affected columns (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter). Fixes v0.12.0 double-encode bug on Postgres; PGLite no-ops. Idempotent.
 - `src/commands/orphans.ts` — `gbrain orphans [--json] [--count] [--include-pseudo]`: surfaces pages with zero inbound wikilinks, grouped by domain. Auto-generated/raw/pseudo pages filtered by default. Also exposed as `find_orphans` MCP operation. Shipped in v0.12.3 (contributed by @knee5).
-- `src/commands/doctor.ts` — `gbrain doctor [--json] [--fast] [--fix] [--dry-run] [--index-audit]`: health checks. v0.12.3 added `jsonb_integrity` + `markdown_body_completeness` reliability checks. v0.14.1: `--fix` delegates inlined cross-cutting rules to `> **Convention:** see [path](path).` callouts (pipes DRY violations into `src/core/dry-fix.ts`); `--fix --dry-run` previews without writing. v0.14.2: `schema_version` check fails loudly when `version=0` (migrations never ran — the #218 `bun install -g` signature) and routes users to `gbrain apply-migrations --yes`; new opt-in `--index-audit` flag (Postgres-only) reports zero-scan indexes from `pg_stat_user_indexes` (informational only, no auto-drop). v0.15.2: every DB check is wrapped in a progress phase; `markdown_body_completeness` runs under a 1s heartbeat timer so 10+ min scans are observable on 50K-page brains. v0.19.1 added `queue_health` (Postgres-only) with two subchecks: stalled-forever active jobs (started_at > 1h) and waiting-depth-per-name > threshold (default 10, override via `GBRAIN_QUEUE_WAITING_THRESHOLD`). Worker-heartbeat subcheck intentionally deferred to follow-up B7 because it needs a `minion_workers` table to produce ground-truth signal. Fix hints point at `gbrain repair-jsonb`, `gbrain sync --force`, `gbrain apply-migrations`, and `gbrain jobs get/cancel <id>`.
-- `src/core/migrate.ts` — schema-migration runner. Owns the `MIGRATIONS` array (source of truth for schema DDL). v0.14.2 extended the `Migration` interface with `sqlFor?: { postgres?, pglite? }` (engine-specific SQL overrides `sql`) and `transaction?: boolean` (set to false for `CREATE INDEX CONCURRENTLY`, which Postgres refuses inside a transaction; ignored on PGLite since it has no concurrent writers). Migration v14 (fix wave) uses a handler branching on `engine.kind` to run CONCURRENTLY on Postgres (with a pre-drop of any invalid remnant via `pg_index.indisvalid`) and plain `CREATE INDEX` on PGLite. v15 bumps `minion_jobs.max_stalled` default 1→5 and backfills existing non-terminal rows.
+- `src/commands/integrity.ts` — `gbrain integrity check|auto|review|extract`: bare-tweet detection, dead-link detection, three-bucket repair (auto-repair / review-queue / skip). `scanIntegrity()` is the shared library function called from `gbrain doctor` (sampled at limit=500) and `cmdCheck` (full scan). v0.22.8: batch-load fast path on Postgres uses `SELECT DISTINCT ON (slug)` in a single SQL query to fix the PgBouncer round-trip timeout (60s → ~6s) while preserving `engine.getAllSlugs()`'s `Set<string>` semantics on multi-source brains. Gated by `engine.kind === 'postgres'` at the call site so PGLite never enters batch; fallback `catch` logs at `GBRAIN_DEBUG=1` so real Postgres errors are diagnosable.
+- `src/commands/doctor.ts` — `gbrain doctor [--json] [--fast] [--fix] [--dry-run] [--index-audit]`: health checks. v0.12.3 added `jsonb_integrity` + `markdown_body_completeness` reliability checks. v0.14.1: `--fix` delegates inlined cross-cutting rules to `> **Convention:** see [path](path).` callouts (pipes DRY violations into `src/core/dry-fix.ts`); `--fix --dry-run` previews without writing. v0.14.2: `schema_version` check fails loudly when `version=0` (migrations never ran — the #218 `bun install -g` signature) and routes users to `gbrain apply-migrations --yes`; new opt-in `--index-audit` flag (Postgres-only) reports zero-scan indexes from `pg_stat_user_indexes` (informational only, no auto-drop). v0.15.2: every DB check is wrapped in a progress phase; `markdown_body_completeness` runs under a 1s heartbeat timer so 10+ min scans are observable on 50K-page brains. v0.19.1 added `queue_health` (Postgres-only) with two subchecks: stalled-forever active jobs (started_at > 1h) and waiting-depth-per-name > threshold (default 10, override via `GBRAIN_QUEUE_WAITING_THRESHOLD`). Worker-heartbeat subcheck intentionally deferred to follow-up B7 because it needs a `minion_workers` table to produce ground-truth signal. Fix hints point at `gbrain repair-jsonb`, `gbrain sync --force`, `gbrain apply-migrations`, and `gbrain jobs get/cancel <id>`. v0.22.12 (#500): `sync_failures` check shows `[CODE=N, ...]` breakdown for both unacked entries (warn) and acked-historical entries (ok), surfacing systemic failure modes (`SLUG_MISMATCH=2685`) instead of a bare count.
+- `src/core/migrate.ts` — schema-migration runner. Owns the `MIGRATIONS` array (source of truth for schema DDL). v0.14.2 extended the `Migration` interface with `sqlFor?: { postgres?, pglite? }` (engine-specific SQL overrides `sql`) and `transaction?: boolean` (set to false for `CREATE INDEX CONCURRENTLY`, which Postgres refuses inside a transaction; ignored on PGLite since it has no concurrent writers). Migration v14 (fix wave) uses a handler branching on `engine.kind` to run CONCURRENTLY on Postgres (with a pre-drop of any invalid remnant via `pg_index.indisvalid`) and plain `CREATE INDEX` on PGLite. v15 bumps `minion_jobs.max_stalled` default 1→5 and backfills existing non-terminal rows. v0.22.6.1: migration v24 (`rls_backfill_missing_tables`) uses `sqlFor: { pglite: '' }` to no-op on PGLite — PGLite has no RLS engine and is single-tenant by definition, and the v24 ALTERs target subagent tables that don't exist in pglite-schema.ts. Closes #395 (contributed by @jdcastro2).
 - `src/core/progress.ts` — Shared bulk-action progress reporter. Writes to stderr. Modes: `auto` (TTY: `\r`-rewriting; non-TTY: plain lines), `human`, `json` (JSONL), `quiet`. Rate-gated by `minIntervalMs` and `minItems`. `startHeartbeat(reporter, note)` helper for single long queries. `child()` composes phase paths. Singleton SIGINT/SIGTERM coordinator emits `abort` events for every live phase. EPIPE defense on both sync throws and stream `'error'` events. Zero dependencies. Introduced in v0.15.2.
 - `src/core/cli-options.ts` — Global CLI flag parser. `parseGlobalFlags(argv)` returns `{cliOpts, rest}` with `--quiet` / `--progress-json` / `--progress-interval=<ms>` stripped. `getCliOptions()` / `setCliOptions()` expose a module-level singleton so commands reach the resolved flags without parameter threading. `cliOptsToProgressOptions()` maps to reporter options. `childGlobalFlags()` returns the flag suffix to append to `execSync('gbrain ...')` calls in migration orchestrators. `OperationContext.cliOpts` extends shared-op dispatch for MCP callers.
+- `src/core/db-lock.ts` (v0.22.13) — generic `tryAcquireDbLock(engine, lockId, ttlMinutes)` over the existing `gbrain_cycle_locks` table. Parameterized lock id so different scopes can nest cleanly: `gbrain-cycle` for the broad cycle (held by `cycle.ts`) and `gbrain-sync` (`SYNC_LOCK_ID` constant) for `performSync`'s narrower writer window. Same UPSERT-with-TTL semantics as the prior cycle-only helper, just generalized. Survives PgBouncer transaction pooling (unlike session-scoped `pg_try_advisory_lock`); crashed holders auto-release once their TTL expires.
+- `src/core/sync-concurrency.ts` (v0.22.13) — single source of truth for the parallel-sync policy. Exports `autoConcurrency(engine, fileCount, override?)` (PGLite always serial; explicit override clamped to >=1; auto path returns `DEFAULT_PARALLEL_WORKERS=4` when `fileCount > AUTO_CONCURRENCY_FILE_THRESHOLD=100`), `shouldRunParallel(workers, fileCount, explicit)` (Q1: explicit `--workers` bypasses the >50-file floor), and `parseWorkers(s)` (rejects `'0'`, `'-3'`, `'foo'`, `'1.5'`, trailing chars — replaces the prior parseInt-with-no-validation in both `sync.ts` and `import.ts`). Used by `performSync`, `performFullSync`, `runImport`, and the Minion `sync` handler so the three sites can no longer drift.
+- `src/commands/sync.ts` — `gbrain sync` CLI + the `performSync` / `performFullSync` library entrypoints (consumed by the autopilot cycle and the Minion sync handler). v0.22.13 (PR #490): `performSync` wraps its body in a `gbrain-sync` writer lock so two concurrent syncs (manual + autopilot, two terminals, two Conductor workspaces) cannot both write `last_commit` and let the last writer win. Head-drift gate after the import phase re-checks `git rev-parse HEAD`; if HEAD moved (someone ran `git checkout` / `git pull` mid-sync), the bookmark refuses to advance. Vanished files now record a failedFiles entry instead of silent-skip — the silent-skip-then-advance pathology that survived prior hardening passes is dead. Worker engines wrap in try/finally so disconnect always fires (panic-path leak fix). Both PGLite-detection sites use `engine.kind === 'pglite'`. CLI accepts `--workers N` (alias `--concurrency N`), validated via `parseWorkers`. Explicit `--workers` bypasses the auto-path file-count floor; auto path defers to `autoConcurrency()`. Banner moved to stderr.
 - `src/core/cycle.ts` — v0.17 brain maintenance cycle primitive. `runCycle(engine: BrainEngine | null, opts: CycleOpts): Promise<CycleReport>` composes 6 phases in semantically-driven order (lint → backlinks → sync → extract → embed → orphans). Three callers: `gbrain dream` CLI, `gbrain autopilot` daemon's inline path, and the Minions `autopilot-cycle` handler (`src/commands/jobs.ts`). One source of truth for what the brain does overnight. Coordination via `gbrain_cycle_locks` DB table (TTL-based; works through PgBouncer transaction pooling, unlike session-scoped `pg_try_advisory_lock`) + `~/.gbrain/cycle.lock` file lock with PID-liveness for PGLite / engine=null mode. `CycleReport.schema_version: "1"` is the stable agent-consumable shape. `PhaseResult.error: { class, code, message, hint?, docs_url? }` is Stripe-API-tier structured failure info. `yieldBetweenPhases` hook awaited between every phase — Minions handler uses this to renew its job lock and prevent v0.14 stall-death regression. Engine nullable: filesystem phases (lint, backlinks) run without DB; DB phases skip with `status: "skipped", reason: "no_database"`. Lock-skip: read-only phase selections (`--phase orphans`) bypass the cycle lock. v0.22.1 (#403): `CycleOpts.signal?: AbortSignal` propagates the worker's abort signal; `checkAborted()` fires between every phase and throws if the signal is aborted (cooperative — can't interrupt a phase mid-execution). v0.22.1 (#417): `runPhaseSync` returns `pagesAffected` via `SyncPhaseResult`; `runCycle` captures it and threads to `runPhaseExtract` as the 4th arg, enabling incremental extract on the cycle path. v0.22.1 (Codex F2): `runPhaseSync` takes `willRunExtractPhase: boolean` and sets `noExtract: phases.includes('extract')` so `gbrain dream --phase sync` doesn't silently lose extraction. v0.22.5 (#475): new `resolveSourceForDir(engine, brainDir)` helper queries `SELECT id FROM sources WHERE local_path = $1 LIMIT 1`; `runPhaseSync` threads result as `sourceId` to `performSync()` so sync reads the per-source `sources.last_commit` anchor instead of the drift-prone global `config.sync.last_commit` key. Bare try/catch lets pre-v0.18 brains fall through to the global key. Closes the prod hang where every autopilot cycle ran a 30-min full reimport because the global anchor commit had been GC'd from git history.
 - `src/commands/dream.ts` — v0.17 `gbrain dream` CLI. ~80-line thin alias over `runCycle`. brainDir resolution requires explicit `--dir` OR `sync.repo_path` config (no more walk-up-cwd-for-.git footgun). Flags: `--dry-run`, `--json`, `--phase <name>`, `--pull`, `--dir <path>`. Exit code 1 on status=failed (partial/warn not fatal — don't page on warnings).
 - `scripts/check-progress-to-stdout.sh` — CI guard against regressing to `\r`-on-stdout progress. Wired into `bun run test` via `scripts/check-progress-to-stdout.sh && bun test` in package.json.
@@ -212,6 +223,10 @@ Key commands added in v0.14.3 (fix wave):
 - `gbrain jobs submit` gains `--max-stalled`, `--backoff-type`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key` — exposing existing `MinionJobInput` fields as first-class CLI flags.
 - `gbrain jobs smoke --sigkill-rescue` — opt-in regression smoke case simulating a killed worker; asserts the v0.14.3 schema default (`max_stalled=5`) actually rescues on first stall.
 
+Key commands added in v0.22.13 (PR #490):
+- `gbrain sync --workers N` (alias `--concurrency N`) — parallelize the import phase using per-worker Postgres engines (small pool of 2 each) with an atomic queue index. Auto-concurrency: defaults to 4 workers when the diff exceeds 100 files. Smaller diffs stay serial. Explicit `--workers` always wins (even on a 30-file diff). PGLite forces serial regardless. Validation rejects `0`, negatives, non-integers loud (replaces the prior silent fall-through to auto-concurrency).
+- `gbrain import --workers N` — same `parseWorkers()` validation as sync; same try/finally worker-engine cleanup. Behavior surface unchanged.
+
 ## Testing
 
 `bun test` runs all tests. After the v0.12.1 release: ~75 unit test files + 8 E2E test files (1412 unit pass, 119 E2E when `DATABASE_URL` is set — skip gracefully otherwise). Unit tests run
@@ -223,7 +238,9 @@ parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redac
 `test/files.test.ts` (MIME/hash), `test/import-file.test.ts` (import pipeline),
 `test/upgrade.test.ts` (schema migrations),
 `test/file-migration.test.ts` (file migration), `test/file-resolver.test.ts` (file resolution),
-`test/import-resume.test.ts` (import checkpoints), `test/migrate.test.ts` (migration; v8/v9 helper-btree-index SQL structural assertions + 1000-row wall-clock fixtures that guard the O(n²)→O(n log n) fix + v0.13.1 assertions on v12/v13 SQL shape, `sqlFor` + `transaction:false` runner semantics, and the `max_stalled DEFAULT 1` regression guard),
+`test/import-resume.test.ts` (import checkpoints), `test/migrate.test.ts` (migration; v8/v9 helper-btree-index SQL structural assertions + 1000-row wall-clock fixtures that guard the O(n²)→O(n log n) fix + v0.13.1 assertions on v12/v13 SQL shape, `sqlFor` + `transaction:false` runner semantics, the `max_stalled DEFAULT 1` regression guard, and v0.22.6.1 v24 `sqlFor.pglite: ''` no-op assertion),
+`test/bootstrap.test.ts` (v0.22.6.1 — bootstrap contract: no-op on fresh install, idempotent across two `initSchema()` calls, no-op on modern brain that already has every probed column, full bootstrap path on simulated pre-v0.18 brain, fresh-install regression guard, pre-v0.13 `links` shape coverage),
+`test/schema-bootstrap-coverage.test.ts` (v0.22.6.1 CI guard — `REQUIRED_BOOTSTRAP_COVERAGE` lists every forward reference in PGLITE_SCHEMA_SQL; the test fails loudly if `applyForwardReferenceBootstrap` skips one. When you add a column-with-index to the embedded schema blob, you extend both arrays or this guard fails. The pattern that broke gbrain ten times in two years is now structurally prevented.),
 `test/setup-branching.test.ts` (setup flow), `test/slug-validation.test.ts` (slug validation),
 `test/storage.test.ts` (storage backends), `test/supabase-admin.test.ts` (Supabase admin),
 `test/yaml-lite.test.ts` (YAML parsing), `test/check-update.test.ts` (version check + update CLI),
@@ -265,6 +282,9 @@ parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redac
 `test/orphans.test.ts` (v0.12.3 orphans command: detection, pseudo filtering, text/json/count outputs, MCP op),
 `test/postgres-engine.test.ts` (v0.12.3 statement_timeout scoping: `sql.begin` + `SET LOCAL` shape, source-level grep guardrail against reintroduced bare `SET statement_timeout`),
 `test/sync.test.ts` (sync logic + v0.12.3 regression guard asserting top-level `engine.transaction` is not called),
+`test/sync-concurrency.test.ts` (v0.22.13 PR #490: 17 cases covering `autoConcurrency()` thresholds + PGLite-forces-serial + explicit-override clamping, `shouldRunParallel()` Q1 explicit-bypasses-floor contract, and `parseWorkers()` validation that rejects `'0'`/`'-3'`/`'foo'`/`'1.5'`/trailing chars),
+`test/sync-parallel.test.ts` (v0.22.13 PR #490: PGLite-routed coverage of the bookmark gate under concurrency request, head-drift gate, vanished-file failure capture, PGLite-stays-serial, and the `gbrain-sync` writer-lock contract — 7 cases),
+`test/sync-failures.test.ts` (v0.22.12: 28 cases pinning `classifyErrorCode` regex coverage for all 12 codes against literal production message strings from `markdown.ts:159-244` and `import-file.ts:199, 347, 352, 401`; `summarizeFailuresByCode` sort + pre-classified-honor; `recordSyncFailures` code-field persistence; `acknowledgeSyncFailures` AcknowledgeResult shape + backfill on pre-v0.22.12 entries),
 `test/doctor.test.ts` (doctor command + v0.12.3 assertions that `jsonb_integrity` scans the four v0.12.0 write sites and `markdown_body_completeness` is present),
 `test/utils.test.ts` (shared SQL utilities + `tryParseEmbedding` null-return and single-warn semantics),
 `test/build-llms.test.ts` (llms.txt/llms-full.txt generator: path resolution, idempotence, spec shape, regen-drift guard, content contract, AGENTS.md install-path mirror, size-budget enforcement — 7 cases),
@@ -275,20 +295,26 @@ parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redac
 `test/skill-manifest.test.ts` (v0.19 skill manifest parser: drift detection, managed-block markers),
 `test/skillify-scaffold.test.ts` (v0.19 `gbrain skillify scaffold` stubs: SKILL.md, script, tests, routing-eval fixtures),
 `test/skillpack-install.test.ts` (v0.19 `gbrain skillpack install` managed-block install / update / no-clobber semantics),
-`test/skillpack-sync-guard.test.ts` (v0.19 sync-guard: bundled skills stay byte-identical to `skills/` source).
+`test/skillpack-sync-guard.test.ts` (v0.19 sync-guard: bundled skills stay byte-identical to `skills/` source),
+`test/http-transport.test.ts` (v0.22.7 HTTP transport: 23 unit cases covering bearer auth + missing/no-Bearer/unknown/revoked + `/health` bypass, F1+F2 round-trip via dispatch.ts, F3 invalid_params, application/json response shape (not SSE), CORS default-deny + allowlist, body cap on Content-Length AND chunked, two-bucket rate limit (refill, exhaust+Retry-After, LRU eviction, TTL prune, pre-auth IP fires before DB), and `mcp_request_log` audit on success + auth_failed).
 
 E2E tests (`test/e2e/`): Run against real Postgres+pgvector. Require `DATABASE_URL`.
 - `bun run test:e2e` runs Tier 1 (mechanical, all operations, no API keys). Includes 9 dedicated cases for the postgres-engine `addLinksBatch` / `addTimelineEntriesBatch` bind path — postgres-js's `unnest()` binding is structurally different from PGLite's and gets its own coverage.
 - `test/e2e/search-quality.test.ts` runs search quality E2E against PGLite (no API keys, in-memory)
 - `test/e2e/graph-quality.test.ts` runs the v0.10.3 knowledge graph pipeline (auto-link via put_page, reconciliation, traversePaths) against PGLite in-memory
 - `test/e2e/postgres-jsonb.test.ts` — v0.12.2 regression test. Round-trips all 5 JSONB write sites (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter) against real Postgres and asserts `jsonb_typeof='object'` plus `->>'key'` returns the expected scalar. The test that should have caught the original double-encode bug.
+- `test/e2e/integrity-batch.test.ts` (v0.22.8) — parity tests for `scanIntegrity`'s batch-load fast path vs sequential. Four cases (dedup, hits, validate, topPages) seed a fixture and assert both paths return identical results. Dedup case uses raw SQL via `getConn().unsafe()` to seed a `(test-source-2, people/alice)` row alongside the default-source row, since `engine.putPage` doesn't take a `source_id`. Pins the codex-caught multi-source overcounting regression.
 - `test/e2e/jsonb-roundtrip.test.ts` — v0.12.3 companion regression against the 4 doctor-scanned JSONB sites. Assertion-level overlap with `postgres-jsonb.test.ts` is intentional defense-in-depth: if doctor's scan surface ever drifts from the actual write surface, one of these tests catches it.
+- `test/e2e/sync.test.ts` (v0.22.12 — `--skip-failed` failure-loop test, alongside the existing 13 happy-path tests): exercises the full chain — broken file → `performSync` returns `blocked_by_failures` with grouped breakdown → `performSync({skipFailed: true})` advances bookmark and returns `AcknowledgeResult` with code summary → second broken file → second cycle. Saves and restores the user's real `~/.gbrain/sync-failures.jsonl` so the test is hermetic on a developer machine. Asserts bookmark gating, JSONL state, dedup across paths, summary aggregation, and the literal doctor-rendering string format. This is the integration test that proves the v0.22.12 chain holds together — unit tests cover the pure functions in isolation, this covers the integration.
 - `test/e2e/upgrade.test.ts` runs check-update E2E against real GitHub API (network required)
 - `test/e2e/minions-shell-pglite.test.ts` (v0.20.4) exercises the PGLite `--follow` inline shell-job path (in-memory, no `DATABASE_URL` required) — the path the consolidated minion-orchestrator skill documents for dev use
 - `test/e2e/openclaw-reference-compat.test.ts` (v0.19) — exercises `check-resolvable` + `skillpack install` against a minimal AGENTS.md workspace fixture (`test/fixtures/openclaw-reference-minimal/`), regression guard for the 107-skill OpenClaw deployment shape
 - `test/e2e/search-swamp.test.ts` (v0.22.0) — reproduces the headline source-swamp case. Seeds a curated `originals/talks/article-outline-fat-code` page against two `wintermute/chat/` pages stuffed with the same multi-word phrase. Asserts the article wins keyword AND vector ranking, that `detail=high` lets the chat swamp re-surface (temporal-query workflow preserved), and that `source_id` passes through the two-stage CTE intact. PGLite in-memory.
 - `test/e2e/search-exclude.test.ts` (v0.22.0) — verifies `test/` + `archive/` pages are hidden by default, that `include_slug_prefixes` opts back in, and that caller-supplied `exclude_slug_prefixes` adds to defaults. Both keyword and vector search paths covered.
 - `test/e2e/engine-parity.test.ts` (v0.22.0) — Postgres ↔ PGLite top-result and result-set parity for `searchKeyword` + `searchVector`. Codex flagged that Postgres ranks pages then picks best chunk while PGLite returns chunks directly — without parity coverage the source-boost fix could pass on PGLite and fail on Postgres. Skips gracefully when `DATABASE_URL` is unset.
+- `test/e2e/postgres-bootstrap.test.ts` (v0.22.6.1) — exercises `PostgresEngine.initSchema()` directly against a fresh real Postgres database. Asserts the bootstrap path is no-op on fresh installs and that SCHEMA_SQL replays cleanly through the engine path (not via the standalone `db.initSchema` from `src/core/db.ts`, which would have produced false-positive coverage). Codex caught the E2E-shape gap during plan review.
+- `test/e2e/http-transport.test.ts` (v0.22.7) — 8 cases against real Postgres covering `gbrain serve --http` end-to-end: bearer auth round-trip, `last_used_at` SQL-level debounce semantics, `mcp_request_log` row insertion on success and auth_failed paths, `/health` DB-down → 503 (DB-probing health check), and the F1+F2+F3 dispatch round-trip with a real operation. Skips gracefully when `DATABASE_URL` is unset.
+- `test/e2e/sync-parallel.test.ts` (v0.22.13 PR #490) — DATABASE_URL-gated. T2: 60-file Postgres sync at concurrency=4 imports all + no connection leak (probes `pg_stat_activity` before/after to confirm worker engines disconnected). P4: 120-file serial-vs-parallel benchmark prints `SYNC_PARALLEL_BENCH N files | serial=Xms | parallel(4)=Yms | speedup=Zx` for CHANGELOG quoting. Asserts parallel ≤ serial × 1.5 (CI-noise tolerant; not a strict speedup gate).
 - Tier 2 (`skills.test.ts`) requires OpenClaw + API keys, runs nightly in CI
 - If `.env.testing` doesn't exist in this directory, check sibling worktrees for one:
   `find ../  -maxdepth 2 -name .env.testing -print -quit` and copy it here if found.

README.md

@@ -80,12 +80,13 @@ Add to `~/.claude/server.json` (Claude Code), Settings > MCP Servers (Cursor), o
 ### Remote MCP (Claude Desktop, Cowork, Perplexity)
 
 ```bash
-ngrok http 8787 --url your-brain.ngrok.app
-bun run src/commands/auth.ts create "claude-desktop"
+gbrain auth create "claude-desktop"            # tokens via the existing CLI
+gbrain serve --http --port 8787                 # built-in HTTP transport (Postgres-only)
+ngrok http 8787 --url your-brain.ngrok.app      # any tunnel works
 claude mcp add gbrain -t http https://your-brain.ngrok.app/mcp -H "Authorization: Bearer TOKEN"
 ```
 
-Per-client guides: [`docs/mcp/`](docs/mcp/DEPLOY.md). ChatGPT requires OAuth 2.1 (not yet implemented).
+Per-client guides: [`docs/mcp/`](docs/mcp/DEPLOY.md). Hardening defaults, env vars, and threat model: [SECURITY.md](SECURITY.md). ChatGPT requires OAuth 2.1 (not yet implemented).
 
 ### Using gbrain with GStack
 
@@ -359,6 +360,30 @@ accumulate rows across separate single-skill installs instead of overwriting eac
 Read [`skills/skillify/SKILL.md`](skills/skillify/SKILL.md) for the full 10-item checklist
 and the anti-patterns it catches.
 
+## Storage tiering: keep bulk content out of git (v0.22.11)
+
+When your brain crosses 100K files and bulk machine-generated content (tweets, articles, transcripts)
+becomes the size driver, declare which directories belong in git and which live in the database only.
+
+```yaml
+# gbrain.yml at the brain repo root
+storage:
+  db_tracked:
+    - people/
+    - companies/
+    - deals/
+  db_only:
+    - media/x/
+    - media/articles/
+    - meetings/transcripts/
+```
+
+`gbrain sync` auto-manages your `.gitignore` for `db_only` paths. `gbrain export --restore-only --repo .`
+repopulates missing files from the database (container restart, fresh clone, accidental rm).
+`gbrain storage status` shows the tier breakdown.
+
+Full guide: [docs/storage-tiering.md](docs/storage-tiering.md).
+
 ## Getting Data In
 
 GBrain ships integration recipes that your agent sets up for you. Each recipe tells the agent what credentials to ask for, how to validate, and what cron to register.
@@ -614,8 +639,11 @@ SEARCH
   gbrain query <question>              Hybrid search (vector + keyword + RRF)
 
 IMPORT
-  gbrain import <dir> [--no-embed]      Import markdown (idempotent)
-  gbrain sync [--repo <path>]           Git-to-brain incremental sync
+  gbrain import <dir> [--no-embed] [--workers N]
+                                        Import markdown (idempotent)
+  gbrain sync [--repo <path>] [--workers N]
+                                        Git-to-brain incremental sync
+                                        (>100-file diffs auto-parallelize 4 workers on Postgres)
   gbrain export [--dir ./out/]          Export to markdown
 
 FILES
@@ -657,6 +685,8 @@ ADMIN
   gbrain doctor --locks                 List idle-in-tx backends (57014 diagnostic, Postgres only)
   gbrain stats                          Brain statistics
   gbrain serve                          MCP server (stdio)
+  gbrain serve --http --port 8787       MCP server (HTTP, Postgres-only, bearer auth)
+  gbrain auth create|list|revoke|test   Token management for the HTTP transport
   gbrain integrations                   Integration recipe dashboard
   gbrain sources list|add|remove|...    Multi-source brain management (v0.18)
   gbrain dream [--dry-run] [--phase N]  One maintenance cycle then exit (cron-friendly)

SECURITY.md

@@ -0,0 +1,168 @@
+# Security
+
+## Reporting Vulnerabilities
+
+If you discover a security issue in GBrain, please report it privately by opening
+a [private security advisory](https://github.com/garrytan/gbrain/security/advisories/new)
+on GitHub.
+
+Do not open a public issue for security vulnerabilities.
+
+## Remote MCP Security
+
+### ⚠️ Do NOT use open OAuth client registration for remote MCP
+
+If you deploy GBrain's MCP server behind an HTTP wrapper with OAuth 2.1
+support, **never allow unauthenticated client registration**. An attacker
+who discovers your server URL can:
+
+1. Register a new OAuth client via `POST /register`
+2. Use `client_credentials` grant to obtain a bearer token
+3. Access all brain data via the MCP tools
+
+### Recommended: `gbrain serve --http`
+
+As of v0.22.7, GBrain ships a built-in HTTP transport that uses the
+existing `access_tokens` table for authentication:
+
+```bash
+# Create a token
+gbrain auth create "my-client"
+
+# Start the HTTP server
+gbrain serve --http --port 8787
+
+# Connect via ngrok, Tailscale, or any tunnel
+ngrok http 8787 --url your-brain.ngrok.app
+```
+
+This is the recommended way to expose GBrain remotely. No OAuth, no
+registration endpoint, no self-service tokens. Tokens are managed
+exclusively via `gbrain auth create/list/revoke`.
+
+### If you must use a custom HTTP wrapper
+
+1. **Require a secret for client registration** — check a header or body
+   parameter before creating new OAuth clients
+2. **Disable `client_credentials` grant** — only allow `authorization_code`
+   with browser-based approval
+3. **Restrict scopes** — never issue tokens with unlimited scope
+4. **Log all token issuance** — alert on unexpected registrations
+5. **Rate-limit registration and token endpoints**
+
+### Token Management
+
+```bash
+gbrain auth create "claude-desktop"   # Create a new token
+gbrain auth list                       # List all tokens
+gbrain auth revoke "claude-desktop"    # Revoke a token
+gbrain auth test <url> --token <tok>   # Smoke-test a remote server
+```
+
+Tokens are stored as SHA-256 hashes in the `access_tokens` table. The
+plaintext token is shown once at creation and never stored.
+
+## `gbrain serve --http` hardening (v0.22.7+)
+
+The built-in HTTP transport ships with several layers of hardening on by
+default. All env vars below are optional; the defaults are intentionally
+conservative.
+
+### Postgres-only
+
+`gbrain serve --http` requires a Postgres engine. PGLite is local-only by
+design and the `access_tokens` / `mcp_request_log` tables don't exist in
+the PGLite schema. Local agents continue to use stdio (`gbrain serve`).
+Running `--http` against a PGLite-backed install fails fast with a clear
+error message at startup.
+
+### CORS
+
+Default-deny: no `Access-Control-Allow-Origin` header is sent unless an
+allowlist is configured. To allow browser-based MCP clients:
+
+```bash
+GBRAIN_HTTP_CORS_ORIGIN=https://claude.ai gbrain serve --http --port 8787
+# Multiple origins: comma-separated
+GBRAIN_HTTP_CORS_ORIGIN=https://claude.ai,https://your.app gbrain serve --http
+```
+
+When the request `Origin` matches the allowlist, the server echoes it
+back in `Access-Control-Allow-Origin` (with `Vary: Origin`). Otherwise no
+CORS header is sent and the browser blocks the request.
+
+### Rate limiting
+
+Two buckets, both stored in a bounded LRU map (default 10K keys, evicts
+least-recently-used on overflow, prunes entries older than 2× the
+window):
+
+| Bucket | When it fires | Default | Env var |
+|---|---|---|---|
+| Pre-auth IP | Before the DB lookup, on every `/mcp` request | 30 req / 60s | `GBRAIN_HTTP_RATE_LIMIT_IP` |
+| Post-auth token | After a valid token is resolved | 60 req / 60s | `GBRAIN_HTTP_RATE_LIMIT_TOKEN` |
+| LRU cap | Maximum distinct keys across both buckets | 10000 | `GBRAIN_HTTP_RATE_LIMIT_LRU` |
+
+On exhaustion the server returns `429 Too Many Requests` with a
+`Retry-After` header.
+
+**Caveat for tunneled deployments (ngrok, Tailscale Funnel, Cloudflare
+Tunnel):** all requests share one egress IP, so the pre-auth IP bucket
+becomes effectively shared by all clients on that tunnel. The
+post-auth token-id bucket is the load-bearing limiter for tunnel-fronted
+deployments.
+
+### Reverse-proxy trust
+
+Disabled by default. To honor `X-Forwarded-For` (or `X-Real-IP`) when
+gbrain runs behind a trusted reverse proxy:
+
+```bash
+GBRAIN_HTTP_TRUST_PROXY=1 gbrain serve --http --port 8787
+```
+
+**Critical safety contract:** only set `GBRAIN_HTTP_TRUST_PROXY=1` when
+**both** of these are true:
+
+1. gbrain is reachable only via a trusted reverse proxy (not directly
+   exposed to the internet on the configured port). The simplest
+   guarantee is to bind gbrain to `127.0.0.1` or a private interface
+   and have the proxy forward to it.
+2. The proxy strips any client-supplied `X-Forwarded-For` and `X-Real-IP`
+   headers, then sets them itself. (nginx with `proxy_set_header
+   X-Forwarded-For $remote_addr` does this; Cloudflare and most cloud
+   load balancers handle it automatically.)
+
+If gbrain is reachable directly AND `GBRAIN_HTTP_TRUST_PROXY=1` is set,
+clients can spoof their IP by sending arbitrary `X-Forwarded-For`
+headers, defeating the pre-auth IP rate limit. Without the flag, gbrain
+ignores all forwarded-for headers and uses the socket peer address,
+which is the safe default for direct-exposure deployments.
+
+### Body size cap
+
+Default 1 MiB, stream-counted (chunked transfers without
+`Content-Length` are still capped). Override:
+
+```bash
+GBRAIN_HTTP_MAX_BODY_BYTES=2097152 gbrain serve --http   # 2 MiB
+```
+
+Over-cap requests get `413 Payload Too Large` immediately, before any
+body is materialized in memory.
+
+### Audit log
+
+Every `/mcp` request writes one row to `mcp_request_log`:
+
+```bash
+psql "$DATABASE_URL" -c \
+  "SELECT created_at, token_name, operation, status, latency_ms
+   FROM mcp_request_log
+   ORDER BY created_at DESC LIMIT 100"
+```
+
+`status` is one of: `success`, `error`, `auth_failed`, `rate_limited`,
+`body_too_large`, `parse_error`, `unknown_method`. Failed-auth rows have
+`token_name = NULL`. Inserts are fire-and-forget so audit failures
+never block requests.

TODOS.md

@@ -1,5 +1,155 @@
 # TODOS
 
+## sync (v0.22.13 follow-up — PR #490 review)
+
+### D-PR490-1 — Plumb resolved `database_url` through `SyncOpts`
+**Priority:** P3
+
+**What:** Add `database_url?: string` (or a richer `resolvedConnection` shape) to
+`SyncOpts` and have the caller (`runSync`, the cycle handler, the jobs handler)
+populate it from the active engine instead of having `performSync` /
+`performFullSync` / `import.ts` each call `loadConfig()` separately. Today every
+sync run hits the config file three times.
+
+**Why:** v0.18 multi-source brains can in principle run different sources against
+different `database_url` endpoints (or different per-source overrides via
+`sources.config_jsonb`). Right now `loadConfig()` returns the global config, and
+that always matches the engine in practice — but the convention papers over a
+real divergence the moment someone wants per-source connection settings. Folding
+the resolution into `SyncOpts` makes the worker-engine creation in `sync.ts` and
+`import.ts` deterministic from `SyncOpts` alone.
+
+**Pros:**
+- Removes 3 redundant `loadConfig()` calls per sync.
+- Makes `performSync` / `performFullSync` side-effect-free with respect to the
+  on-disk config file.
+- Sets up for per-source `database_url` overrides without further refactor.
+- Makes the v0.22.13 belt-and-suspenders fallback (PR #490 Q3) cleaner — no
+  more `!config?.database_url` short-circuit inside the parallel branch.
+
+**Cons:**
+- API-shape change to `SyncOpts` (mild; not externally exported).
+- Touching three callers (`runSync`, jobs handler, `cycle.ts` `runPhaseSync`).
+- Only worth doing when paired with a per-source override story; otherwise
+  it's just plumbing.
+
+**Context:** Surfaced during the PR #490 plan-eng-review (parallel sync).
+Deferred because it isn't on the v0.22.13 critical path. The same pattern would
+benefit the cycle handler and the autopilot daemon. See the plan-eng-review
+decisions log: A4 = "Defer; file as TODO."
+
+**Depends on / blocked by:** Nothing structural. Best paired with the v0.18
+per-source `config_jsonb` work if/when that lands.
+
+## sync error-code classification (PR #501 follow-ups)
+
+### Plumb structured `ParseValidationCode` through `ImportResult`
+**Priority:** P2
+
+**What:** Replace the regex-on-error-message path in `src/core/sync.ts:classifyErrorCode`
+with a structured `code` field threaded through `ImportResult` from the parse layer.
+
+Three changes:
+1. `src/core/import-file.ts:362` — call `parseMarkdown(content, relativePath, { validate: true, expectedSlug })`
+   so `parsed.errors[0].code` is populated.
+2. `src/core/import-file.ts` — add `code?: string` to `ImportResult`. Promote the
+   structured code (or `'SLUG_MISMATCH'` when the existing expectedSlug check trips)
+   into the result envelope alongside `error`.
+3. `src/commands/sync.ts:488` — extend `failedFiles` shape with `code?: string`.
+   `recordSyncFailures` already accepts the field; the only thing missing is the
+   capture site populating it.
+4. `src/core/sync.ts:classifyErrorCode` — keep as a fallback for un-coded errors
+   (DB exceptions, generic catches). Primary path reads the structured code.
+
+**Why:** The repo already has `ParseValidationCode` + `ParseValidationError` in
+`src/core/markdown.ts:5-18`, and three other consumers (`src/commands/lint.ts:72`,
+`src/commands/frontmatter.ts:148`, `src/core/brain-writer.ts:314`) read structured
+errors directly. Sync is the outlier — it calls `parseMarkdown` without validation
+and reverse-engineers codes via regex. PR #501 shipped that regex out of pragmatism;
+this TODO removes ~50% of `classifyErrorCode` and eliminates a class of false-positives.
+
+**Pros:**
+- One source of truth for parse codes (the enum in `markdown.ts`).
+- Eliminates regex fragility — adding a new validation code in `markdown.ts`
+  automatically flows to sync without a new regex.
+- Closes the case where canonical messages (`File is empty...`, `No closing ---...`)
+  don't match aspirational regex patterns.
+
+**Cons:** Touches `ImportResult` interface, which ripples through `src/commands/import.ts:105`,
+`src/commands/sync.ts:498-510`, `src/core/cycle.ts`, brain-writer reconciler.
+
+**Context:** PR #501 documented this as P3 in the eng review at
+`~/.claude/plans/then-codex-synchronous-toucan.md`. Codex's outside-voice review
+agreed independently. The fix is small — ~50 lines including tests + downstream
+call sites — and it's the correct architectural endpoint.
+
+**Effort:** M (human: ~2 hr / CC: ~20 min).
+
+**Depends on / blocked by:** Nothing.
+
+### CHANGELOG migration note for `acknowledgeSyncFailures()` shape change
+**Priority:** P0 — required at /ship time
+
+**What:** When PR #501 ships, the release CHANGELOG entry MUST include this
+`### For contributors` block:
+
+```markdown
+### For contributors
+
+`acknowledgeSyncFailures()` now returns `{count, summary}` instead of `number`.
+If you import this directly from `gbrain/sync`, replace `n` with `result.count`
+and use `result.summary` for the new code-grouped breakdown.
+```
+
+**Why:** The function is exported from `src/core/sync.ts:433` and reachable via
+the package exports map. External TS consumers (gbrain-evals, host agent forks)
+that imported it got `number` and now get an object — silent type break.
+
+**Effort:** XS (human: ~1 min). Just don't forget.
+
+**Depends on / blocked by:** PR #501 ship.
+
+### Concurrent-safe ack of `~/.gbrain/sync-failures.jsonl`
+**Priority:** P3
+
+**What:** Two concurrent `gbrain sync` runs hitting `acknowledgeSyncFailures()`
+can clobber each other. The function does a whole-file `writeFileSync` rewrite
+(`src/core/sync.ts:433-455`); `recordSyncFailures()` does independent
+`appendFileSync` (`src/core/sync.ts:395-416`). Concurrent ack + append can lose rows.
+
+**Why:** Pre-existing — predates PR #501. Real risk only on autopilot setups where
+multiple sync invocations might overlap (rare today, more likely as multi-source
+sync matures).
+
+**Fix sketch:** Atomic rename pattern (write to `sync-failures.jsonl.tmp`, then
+`renameSync`) plus a file lock for the read-modify-write cycle. Or move the
+acknowledged-set to the DB.
+
+**Effort:** S (human: ~1 hr / CC: ~10 min).
+
+**Depends on / blocked by:** Nothing.
+
+## test-infra
+
+### Parallel-load timeout flake on v0.21 PGLite-heavy tests
+**Priority:** P0
+
+**What:** 22 tests added in v0.21.0 (Code Cathedral II) consistently fail in the full `bun test` run with timeout-pattern elapsed times of 7-10s, but pass in isolation. Every failing test calls `engine.initSchema()` in `beforeAll` without a timeout extension. Under parallel load (168 test files now run concurrently after v0.21 added ~24 new files), `initSchema` exceeds bun's default 5s `beforeAll` timeout.
+
+Affected files include (non-exhaustive): `test/sync-strategy.test.ts`, `test/cathedral-ii-brainbench.test.ts`, `test/code-edges.test.ts`, `test/reindex-code.test.ts`, `test/reconcile-links.test.ts`, `test/two-pass.test.ts`, `test/parent-symbol-path.test.ts`, `test/pglite-v0_19.test.ts`.
+
+**Why:** Currently triaged as "skip pre-existing, ship anyway" but that's not a real fix. Blocks /ship for anyone whose CHANGELOG-time test run sees them.
+
+**Pros:** Fixing it lets /ship run cleanly without manual triage every release.
+
+**Cons:** ~22 file edits adding `beforeAll(async () => {...}, 30000)` is mechanical but dull.
+
+**Context:** Same pattern fixed in v0.20.5 wave for `test/e2e/minions-shell-pglite.test.ts`. Single-file repro: each fails in `bun test`, passes in `bun test <file>`. Reproduces with my changes stashed, so it's on master.
+
+**Effort:** S (human: ~30 min / CC: ~5 min). Mechanical: grep for `beforeAll(async () => {` in affected files, add `, 30000)` argument.
+
+**Depends on / blocked by:** Nothing.
+
 ## resolver / check-resolvable (v0.22.4 follow-ups)
 
 ### D10 — Extend `check-resolvable` to parse RESOLVER.md disambiguation rules
@@ -564,3 +714,90 @@ iteration's residuals.
 **Effort estimate:** S (human: ~2 hr / CC: ~10 min).
 **Priority:** P3.
 **Depends on:** The above caller-opt-in retry (#1) is the natural co-lander since both touch the same error-classification surface.
+
+## remote MCP / HTTP transport (v0.22.7 follow-ups)
+
+### Audit-log write amplification on rejected `/mcp` traffic
+**What:** `src/mcp/http-transport.ts` writes a row to `mcp_request_log` for every
+incoming `/mcp` request, including rate-limited (429), oversized (413), and
+auth-failed (401) traffic. Under sustained attack the IP rate limit caps audit
+writes per IP at 30/min, but at scale (10K distinct IPs) that's still 300K
+inserts/min. Two follow-ups: (1) instrument the audit-write rate so we can see
+the actual production volume; (2) consider a separate "rejected" table or
+sampling for failed-auth rows so the success-path audit table doesn't get
+swamped.
+
+**Why:** Codex flagged this during the v0.22.7 ship adversarial review. We kept
+the full audit on purpose — forensic data of an attack is valuable — but want
+to revisit once we have real volume numbers.
+
+**Pros:** Bounds DB write volume under attack. Keeps the success-path audit
+table small enough for fast queries.
+
+**Cons:** Adds a second table or a sampling rule. Not free complexity. Probably
+not worth it until production hits a real attack pattern.
+
+**Context:** `src/mcp/http-transport.ts:222,235,245` (the three audit-on-reject
+call sites) + `src/schema.sql:342` (the unbounded table).
+
+**Effort estimate:** M (human: ~half day / CC: ~30 min once we have volume data).
+**Priority:** P3 — wait for evidence.
+**Depends on:** Production telemetry on `mcp_request_log` insert rate.
+
+### `validateParams` doesn't check enum values or array item types
+**What:** `src/mcp/dispatch.ts:27` (extracted from `src/mcp/server.ts` in
+v0.22.7) only checks top-level JS types. Operations declare `enum` constraints
+(e.g. `direction: 'in' | 'out' | 'both'`) and array `items: { type: ... }`
+schemas in `src/core/operations.ts`, but `validateParams` ignores both. Bad
+inputs still reach handlers — concretely, an invalid `direction` falls through
+the engine's else branch at `src/core/postgres-engine.ts:954`, widening
+traversal unexpectedly; malformed `pages_updated` arrays could be written as
+garbage JSONB.
+
+**Why:** Codex flagged this during the v0.22.7 ship adversarial review. The
+validator was lifted verbatim from the pre-existing stdio path during the
+dispatch.ts extraction — same gap exists on the stdio MCP server today, so
+this isn't a v0.22.7 regression. Still worth tightening, since "shared
+validation" is now the architectural guarantee both transports rely on.
+
+**Pros:** Better defense-in-depth at the MCP boundary. Catches malformed agent
+inputs before the engine layer has to.
+
+**Cons:** Need to walk every operation's param schema and decide which enum
+violations are user-facing errors vs internal bugs. May need a typed Zod-style
+schema layer to do this cleanly.
+
+**Context:** `src/mcp/dispatch.ts:27` + `src/core/operations.ts` (param defs).
+Same gap pre-existed on stdio MCP path.
+
+**Effort estimate:** M (human: ~half day / CC: ~30 min if we use the existing
+ParamDef shape; XL if a Zod migration is the chosen direction).
+**Priority:** P2.
+**Depends on:** Whether we want to keep the lightweight ParamDef shape or
+migrate to typed schemas.
+
+### Streaming MCP tool support (re-add SSE based on Accept header)
+**What:** v0.22.7 dropped SSE entirely from `gbrain serve --http` because no
+current MCP tool streams. When the first streaming tool ships (long-running
+agent delegation as an MCP tool, `resources/subscribe`, `sampling/createMessage`),
+re-add SSE in `/mcp` based on the `Accept` header per the Streamable HTTP
+transport spec. ~30 lines + spec compliance test.
+
+**Why:** Removing SSE simplified the v0.22.7 transport (one response path,
+fewer test cases). Adding it back when actually needed is cheap and keeps the
+code lean in the meantime.
+
+**Effort estimate:** S (human: ~2 hr / CC: ~15 min).
+**Priority:** P3 — wait for the first streaming tool.
+**Depends on:** A streaming MCP tool actually existing.
+
+### `access_tokens.scopes` enforcement
+**What:** The `access_tokens` schema has had a `scopes TEXT[]` column since
+migration v4 (`src/core/migrate.ts:84`), but nothing enforces it. v0.22.7's
+`gbrain auth create` doesn't accept a `--scopes` flag, and `dispatchToolCall`
+doesn't gate on scopes. Adding per-tool scope enforcement would let
+"claude-desktop-readonly" and "ingest-only" tokens exist.
+
+**Effort estimate:** M (human: ~1 day / CC: ~30 min for the schema-aware gate).
+**Priority:** P3.
+**Depends on:** Nothing.

VERSION

@@ -1 +1 @@
-0.22.5
+0.22.13

bun.lock

@@ -20,6 +20,7 @@
       },
       "devDependencies": {
         "@types/bun": "latest",
+        "bun-types": "^1.3.13",
         "typescript": "^5.6.0",
       },
     },
@@ -220,7 +221,7 @@
 
     "@types/bun": ["@types/bun@1.3.11", "", { "dependencies": { "bun-types": "1.3.11" } }, "sha512-5vPne5QvtpjGpsGYXiFyycfpDF2ECyPcTSsFBMa0fraoxiQyMJ3SmuQIGhzPg2WJuWxVBoxWJ2kClYTcw/4fAg=="],
 
-    "@types/node": ["@types/node@18.19.130", "", { "dependencies": { "undici-types": "~5.26.4" } }, "sha512-GRaXQx6jGfL8sKfaIDD6OupbIHBr9jv7Jnaml9tB7l4v068PAOXqfcujMMo5PhbIs6ggR1XODELqahT2R8v0fg=="],
+    "@types/node": ["@types/node@25.5.2", "", { "dependencies": { "undici-types": "~7.18.0" } }, "sha512-tO4ZIRKNC+MDWV4qKVZe3Ql/woTnmHDr5JD8UI5hn2pwBrHEwOEMZK7WlNb5RKB6EoJ02gwmQS9OrjuFnZYdpg=="],
 
     "@types/node-fetch": ["@types/node-fetch@2.6.13", "", { "dependencies": { "@types/node": "*", "form-data": "^4.0.4" } }, "sha512-QGpRVpzSaUs30JBSGPjOg4Uveu384erbHBoT1zeONvyCfwQxIkUshLAOqN/k9EjGviPRmWTTe6aH2qySWKTVSw=="],
 
@@ -242,7 +243,7 @@
 
     "bowser": ["bowser@2.14.1", "", {}, "sha512-tzPjzCxygAKWFOJP011oxFHs57HzIhOEracIgAePE4pqB3LikALKnSzUyU4MGs9/iCEUuHlAJTjTc5M+u7YEGg=="],
 
-    "bun-types": ["bun-types@1.3.11", "", { "dependencies": { "@types/node": "*" } }, "sha512-1KGPpoxQWl9f6wcZh57LvrPIInQMn2TQ7jsgxqpRzg+l0QPOFvJVH7HmvHo/AiPgwXy+/Thf6Ov3EdVn1vOabg=="],
+    "bun-types": ["bun-types@1.3.13", "", { "dependencies": { "@types/node": "*" } }, "sha512-QXKeHLlOLqQX9LgYaHJfzdBaV21T63HhFJnvuRCcjZiaUDpbs5ED1MgxbMra71CsryN/1dAoXuJJJwIv/2drVA=="],
 
     "bytes": ["bytes@3.1.2", "", {}, "sha512-/Nf7TyzTx6S3yRJObOAV7956r8cr2+Oj8AC5dt8wSP3BQAoeX58NoHyCU8P8zGkNXStjTSi6fzO6F0pBdcYbEg=="],
 
@@ -466,7 +467,7 @@
 
     "typescript": ["typescript@5.9.3", "", { "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver" } }, "sha512-jl1vZzPDinLr9eUt3J/t7V6FgNEw9QjvBPdysz9KfQDD41fQrC2Y4vKQdiaUpFT4bXlb1RHhLpp8wtm6M5TgSw=="],
 
-    "undici-types": ["undici-types@5.26.5", "", {}, "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA=="],
+    "undici-types": ["undici-types@7.18.2", "", {}, "sha512-AsuCzffGHJybSaRrmr5eHr81mwJU3kjw6M+uprWvCXiNeN9SOGwQ3Jn8jb8m3Z6izVgknn1R0FTCEAP2QrLY/w=="],
 
     "unpipe": ["unpipe@1.0.0", "", {}, "sha512-pjy2bYhSsufwWlKwPc+l3cN7+wuJlK6uz0YdJEOlQDbl6jo/YlPi4mb8agUkVC8BF7V8NuzeyPNqRksA3hztKQ=="],
 
@@ -488,30 +489,32 @@
 
     "zod-to-json-schema": ["zod-to-json-schema@3.25.2", "", { "peerDependencies": { "zod": "^3.25.28 || ^4" } }, "sha512-O/PgfnpT1xKSDeQYSCfRI5Gy3hPf91mKVDuYLUHZJMiDFptvP41MSnWofm8dnCm0256ZNfZIM7DSzuSMAFnjHA=="],
 
+    "@anthropic-ai/sdk/@types/node": ["@types/node@18.19.130", "", { "dependencies": { "undici-types": "~5.26.4" } }, "sha512-GRaXQx6jGfL8sKfaIDD6OupbIHBr9jv7Jnaml9tB7l4v068PAOXqfcujMMo5PhbIs6ggR1XODELqahT2R8v0fg=="],
+
     "@aws-crypto/sha1-browser/@smithy/util-utf8": ["@smithy/util-utf8@2.3.0", "", { "dependencies": { "@smithy/util-buffer-from": "^2.2.0", "tslib": "^2.6.2" } }, "sha512-R8Rdn8Hy72KKcebgLiv8jQcQkXoLMOGGv5uI1/k0l+snqkOzQ1R0ChUBCxWMlBsFMekWjq0wRudIweFs7sKT5A=="],
 
     "@aws-crypto/sha256-browser/@smithy/util-utf8": ["@smithy/util-utf8@2.3.0", "", { "dependencies": { "@smithy/util-buffer-from": "^2.2.0", "tslib": "^2.6.2" } }, "sha512-R8Rdn8Hy72KKcebgLiv8jQcQkXoLMOGGv5uI1/k0l+snqkOzQ1R0ChUBCxWMlBsFMekWjq0wRudIweFs7sKT5A=="],
 
     "@aws-crypto/util/@smithy/util-utf8": ["@smithy/util-utf8@2.3.0", "", { "dependencies": { "@smithy/util-buffer-from": "^2.2.0", "tslib": "^2.6.2" } }, "sha512-R8Rdn8Hy72KKcebgLiv8jQcQkXoLMOGGv5uI1/k0l+snqkOzQ1R0ChUBCxWMlBsFMekWjq0wRudIweFs7sKT5A=="],
 
-    "@types/node-fetch/@types/node": ["@types/node@25.5.2", "", { "dependencies": { "undici-types": "~7.18.0" } }, "sha512-tO4ZIRKNC+MDWV4qKVZe3Ql/woTnmHDr5JD8UI5hn2pwBrHEwOEMZK7WlNb5RKB6EoJ02gwmQS9OrjuFnZYdpg=="],
-
-    "bun-types/@types/node": ["@types/node@25.5.2", "", { "dependencies": { "undici-types": "~7.18.0" } }, "sha512-tO4ZIRKNC+MDWV4qKVZe3Ql/woTnmHDr5JD8UI5hn2pwBrHEwOEMZK7WlNb5RKB6EoJ02gwmQS9OrjuFnZYdpg=="],
+    "@types/bun/bun-types": ["bun-types@1.3.11", "", { "dependencies": { "@types/node": "*" } }, "sha512-1KGPpoxQWl9f6wcZh57LvrPIInQMn2TQ7jsgxqpRzg+l0QPOFvJVH7HmvHo/AiPgwXy+/Thf6Ov3EdVn1vOabg=="],
 
     "form-data/mime-types": ["mime-types@2.1.35", "", { "dependencies": { "mime-db": "1.52.0" } }, "sha512-ZDY+bPm5zTTF+YpCrAU9nK0UgICYPT0QtT1NZWFv4s++TNkcgVaT0g6+4R2uI4MjQjzysHB1zxuWL50hzaeXiw=="],
 
+    "openai/@types/node": ["@types/node@18.19.130", "", { "dependencies": { "undici-types": "~5.26.4" } }, "sha512-GRaXQx6jGfL8sKfaIDD6OupbIHBr9jv7Jnaml9tB7l4v068PAOXqfcujMMo5PhbIs6ggR1XODELqahT2R8v0fg=="],
+
+    "@anthropic-ai/sdk/@types/node/undici-types": ["undici-types@5.26.5", "", {}, "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA=="],
+
     "@aws-crypto/sha1-browser/@smithy/util-utf8/@smithy/util-buffer-from": ["@smithy/util-buffer-from@2.2.0", "", { "dependencies": { "@smithy/is-array-buffer": "^2.2.0", "tslib": "^2.6.2" } }, "sha512-IJdWBbTcMQ6DA0gdNhh/BwrLkDR+ADW5Kr1aZmd4k3DIF6ezMV4R2NIAmT08wQJ3yUK82thHWmC/TnK/wpMMIA=="],
 
     "@aws-crypto/sha256-browser/@smithy/util-utf8/@smithy/util-buffer-from": ["@smithy/util-buffer-from@2.2.0", "", { "dependencies": { "@smithy/is-array-buffer": "^2.2.0", "tslib": "^2.6.2" } }, "sha512-IJdWBbTcMQ6DA0gdNhh/BwrLkDR+ADW5Kr1aZmd4k3DIF6ezMV4R2NIAmT08wQJ3yUK82thHWmC/TnK/wpMMIA=="],
 
     "@aws-crypto/util/@smithy/util-utf8/@smithy/util-buffer-from": ["@smithy/util-buffer-from@2.2.0", "", { "dependencies": { "@smithy/is-array-buffer": "^2.2.0", "tslib": "^2.6.2" } }, "sha512-IJdWBbTcMQ6DA0gdNhh/BwrLkDR+ADW5Kr1aZmd4k3DIF6ezMV4R2NIAmT08wQJ3yUK82thHWmC/TnK/wpMMIA=="],
 
-    "@types/node-fetch/@types/node/undici-types": ["undici-types@7.18.2", "", {}, "sha512-AsuCzffGHJybSaRrmr5eHr81mwJU3kjw6M+uprWvCXiNeN9SOGwQ3Jn8jb8m3Z6izVgknn1R0FTCEAP2QrLY/w=="],
-
-    "bun-types/@types/node/undici-types": ["undici-types@7.18.2", "", {}, "sha512-AsuCzffGHJybSaRrmr5eHr81mwJU3kjw6M+uprWvCXiNeN9SOGwQ3Jn8jb8m3Z6izVgknn1R0FTCEAP2QrLY/w=="],
-
     "form-data/mime-types/mime-db": ["mime-db@1.52.0", "", {}, "sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg=="],
 
+    "openai/@types/node/undici-types": ["undici-types@5.26.5", "", {}, "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA=="],
+
     "@aws-crypto/sha1-browser/@smithy/util-utf8/@smithy/util-buffer-from/@smithy/is-array-buffer": ["@smithy/is-array-buffer@2.2.0", "", { "dependencies": { "tslib": "^2.6.2" } }, "sha512-GGP3O9QFD24uGeAXYUjwSTXARoqpZykHadOmA8G5vfJPK0/DC67qa//0qvqrJzL1xc8WQWX7/yc7fwudjPHPhA=="],
 
     "@aws-crypto/sha256-browser/@smithy/util-utf8/@smithy/util-buffer-from/@smithy/is-array-buffer": ["@smithy/is-array-buffer@2.2.0", "", { "dependencies": { "tslib": "^2.6.2" } }, "sha512-GGP3O9QFD24uGeAXYUjwSTXARoqpZykHadOmA8G5vfJPK0/DC67qa//0qvqrJzL1xc8WQWX7/yc7fwudjPHPhA=="],

docs/mcp/ALTERNATIVES.md

@@ -1,8 +1,9 @@
 # Remote MCP Deployment Options
 
 GBrain's MCP server runs via `gbrain serve` (stdio transport). To make it
-accessible from other devices and AI clients, you need an HTTP wrapper and
-a public tunnel. Here are your options.
+accessible from other devices and AI clients, run `gbrain serve --http`
+(built-in HTTP transport with bearer auth, Postgres-only ... see
+[DEPLOY.md](DEPLOY.md)) behind a public tunnel. Here are your tunnel options.
 
 ## ngrok (recommended)
 
@@ -13,8 +14,9 @@ a public tunnel. Here are your options.
 # 1. Install ngrok
 brew install ngrok
 
-# 2. Start your MCP server (behind an HTTP wrapper)
-# See docs/mcp/DEPLOY.md for the server setup
+# 2. Start the built-in HTTP transport
+gbrain serve --http --port 8787
+# See docs/mcp/DEPLOY.md for token setup
 
 # 3. Expose via ngrok
 ngrok http 8787 --url your-brain.ngrok.app
@@ -59,6 +61,7 @@ Both run Bun natively. No bundling, no Deno, no cold start, no timeout limits.
 | All 30 operations | Yes | Yes | Yes |
 | Setup time | 5 min | 10 min | 15 min |
 
-**Note:** `gbrain serve --http` (built-in HTTP transport) is planned but not yet
-implemented. Currently, remote MCP requires a custom HTTP wrapper around `gbrain serve`.
-See [DEPLOY.md](DEPLOY.md) for details.
+**Note:** `gbrain serve --http` is the built-in HTTP transport (v0.22.7+). Bearer auth
+against the `access_tokens` table, default-deny CORS, two-bucket rate limit, body cap,
+per-request audit log. Postgres-only by design (PGLite is local-only). See
+[DEPLOY.md](DEPLOY.md) and [SECURITY.md](../../SECURITY.md) for env vars and tunables.

docs/mcp/CLAUDE_CODE.md

@@ -21,7 +21,7 @@ claude mcp add gbrain -t http \
 ```
 
 Replace `YOUR-DOMAIN` with your ngrok domain and `YOUR_TOKEN` with a token
-from `bun run src/commands/auth.ts create "claude-code"`.
+from `gbrain auth create "claude-code"`.
 
 ## Verify
 

docs/mcp/CLAUDE_COWORK.md

@@ -12,7 +12,7 @@ For Team/Enterprise plans, an org Owner adds the connector:
    https://YOUR-DOMAIN.ngrok.app/mcp
    ```
 3. Add Bearer token authentication in Advanced Settings
-   (create one with `bun run src/commands/auth.ts create "cowork"`)
+   (create one with `gbrain auth create "cowork"`)
 4. Save
 
 Note: Cowork connects from Anthropic's cloud, not your device. Your server

docs/mcp/CLAUDE_DESKTOP.md

@@ -16,7 +16,7 @@ Remote HTTP servers must be added through the GUI.
    Replace `YOUR-DOMAIN` with your ngrok domain (see
    [ngrok-tunnel recipe](../../recipes/ngrok-tunnel.md) for setup).
 5. Set authentication to **Bearer Token** and paste your token
-   (create one with `bun run src/commands/auth.ts create "claude-desktop"`)
+   (create one with `gbrain auth create "claude-desktop"`)
 6. Save
 
 ## Verify

docs/mcp/DEPLOY.md

@@ -1,8 +1,13 @@
 # Deploy GBrain Remote MCP Server
 
+> **v0.22.7+:** Use `gbrain serve --http` for remote access. It includes built-in
+> bearer token auth, default-deny CORS, two-bucket rate limiting, body cap, and
+> per-request audit log. **Postgres-only** (PGLite is local-only by design).
+> See [SECURITY.md](../../SECURITY.md) for env vars and tunable defaults.
+
 Access your brain from any device, any AI client. GBrain's MCP server runs locally
-via `gbrain serve` (stdio). For remote access, wrap it in an HTTP server behind a
-public tunnel.
+via `gbrain serve` (stdio). For remote access, expose it via the built-in HTTP
+transport behind a public tunnel.
 
 ## Two Paths
 
@@ -13,21 +18,23 @@ gbrain serve
 ```
 
 Works with Claude Code, Cursor, Windsurf, and any MCP client that supports stdio.
-No server, no tunnel, no token needed.
+No server, no tunnel, no token needed. Works on both PGLite and Postgres engines.
 
-### Remote (any device, any AI client)
+### Remote (any device, any AI client) — Postgres only
 
 ```
 Your AI client (Claude Desktop, Perplexity, etc.)
   → ngrok tunnel (https://YOUR-DOMAIN.ngrok.app)
-  → Your HTTP server (wraps gbrain serve)
-  → Supabase Postgres (via pooler connection string)
+  → gbrain serve --http  (built-in transport with bearer auth)
+  → Postgres (pooler connection or self-hosted)
 ```
 
 This requires:
-1. A machine running `gbrain serve` behind an HTTP wrapper
-2. A public tunnel (ngrok, Tailscale, or cloud host)
-3. Bearer token auth for security
+1. A Postgres-backed brain (the `access_tokens` table only exists on Postgres;
+   running `gbrain serve --http` against a PGLite install fails fast at startup)
+2. A machine running `gbrain serve --http`
+3. A public tunnel (ngrok, Tailscale, or cloud host)
+4. A bearer token created via `gbrain auth create <name>`
 
 ## Remote Setup
 
@@ -46,13 +53,13 @@ ngrok http 8787 --url your-brain.ngrok.app  # Hobby tier for fixed domain
 
 ```bash
 # Create a token for each client
-bun run src/commands/auth.ts create "claude-desktop"
+gbrain auth create "claude-desktop"
 
 # List all tokens
-bun run src/commands/auth.ts list
+gbrain auth list
 
 # Revoke a token
-bun run src/commands/auth.ts revoke "claude-desktop"
+gbrain auth revoke "claude-desktop"
 ```
 
 Tokens are per-client. Create one for each device/app. Revoke individually
@@ -68,7 +75,7 @@ if compromised. Tokens are stored SHA-256 hashed in your database.
 ### 4. Verify
 
 ```bash
-bun run src/commands/auth.ts test \
+gbrain auth test \
   https://YOUR-DOMAIN.ngrok.app/mcp \
   --token YOUR_TOKEN
 ```
@@ -96,7 +103,7 @@ Funnel, and cloud hosts (Fly.io, Railway).
 Include the Authorization header: `Authorization: Bearer YOUR_TOKEN`
 
 **"invalid_token" error**
-Run `bun run src/commands/auth.ts list` to see active tokens.
+Run `gbrain auth list` to see active tokens.
 
 **"service_unavailable" error**
 Database connection failed. Check your Supabase dashboard for outages.

docs/mcp/PERPLEXITY.md

@@ -10,7 +10,7 @@ Perplexity Computer supports remote MCP servers with bearer token authentication
    - **URL:** `https://YOUR-DOMAIN.ngrok.app/mcp`
    - **Authentication:** API Key / Bearer Token
    - **Token:** your GBrain access token
-     (create one with `bun run src/commands/auth.ts create "perplexity"`)
+     (create one with `gbrain auth create "perplexity"`)
 4. Save
 
 Replace `YOUR-DOMAIN` with your ngrok domain (see

docs/storage-tiering.md

@@ -0,0 +1,210 @@
+# Storage Tiering: db-tracked vs db-only directories
+
+## Overview
+
+GBrain supports storage tiering to separate version-controlled content from bulk machine-generated data. This prevents git repositories from becoming bloated with large amounts of automatically generated content while still preserving it in the database.
+
+> Note on naming: prior to v0.22.11 the keys were `git_tracked` / `supabase_only`. The canonical names are now `db_tracked` / `db_only` (engine-agnostic — works on both PGLite and Postgres). The deprecated keys still load with a once-per-process warning. Run `gbrain doctor --fix` for an automated rename when that path lands.
+
+## Configuration
+
+Add a `storage` section to your `gbrain.yml` file in the brain repository root:
+
+```yaml
+storage:
+  # Directories that are version-controlled (human-edited, committed to git).
+  db_tracked:
+    - people/
+    - companies/
+    - deals/
+    - concepts/
+    - yc/
+    - ideas/
+    - projects/
+
+  # Directories persisted via the brain database only (bulk machine-generated
+  # content). Written to disk as a local cache but not committed to git;
+  # `gbrain sync` auto-manages .gitignore for these paths. `gbrain export
+  # --restore-only` repopulates missing files from the database.
+  db_only:
+    - media/x/
+    - media/articles/
+    - meetings/transcripts/
+```
+
+Path requirements:
+
+- Each directory must end with `/` for canonical form. The validator auto-normalizes missing trailing slashes (one-time info note shows what changed).
+- A directory cannot appear in both tiers — that's a tier-overlap error and `loadStorageConfig` throws `StorageConfigError`. Edit `gbrain.yml` to remove the overlap and try again.
+
+## Behavior Changes
+
+### 1. `gbrain sync` — automatic .gitignore management
+
+When storage configuration is present, `gbrain sync` automatically manages `.gitignore` entries on every successful sync:
+
+- Adds missing `db_only` directory patterns to `.gitignore`.
+- Idempotent — re-running adds no duplicate entries.
+- Stable comment header so the managed block is grep-able.
+- Skipped on `--dry-run` (don't mutate disk in preview mode).
+- Skipped on `blocked_by_failures` status (sync state is inconsistent).
+- Skipped when the repo is a git submodule (`.git` is a file, not a directory) — submodule .gitignore changes don't survive parent updates. A warning explains.
+- Skipped entirely when `GBRAIN_NO_GITIGNORE=1` is set (escape hatch for shared-repo setups where a maintainer wants gbrain to leave .gitignore alone).
+- Failures (write permission denied, etc.) are caught and logged, never crash sync.
+
+Example `.gitignore` addition:
+
+```gitignore
+# Auto-managed by gbrain (db_only directories)
+media/x/
+media/articles/
+meetings/transcripts/
+```
+
+### 2. `gbrain export --restore-only` — repopulate missing db_only files
+
+```bash
+# Restore only missing db_only files from the database.
+gbrain export --restore-only --repo /path/to/brain
+
+# Filter by page type.
+gbrain export --restore-only --type media --repo /path/to/brain
+
+# Filter by slug prefix.
+gbrain export --restore-only --slug-prefix media/x/ --repo /path/to/brain
+
+# Combine filters.
+gbrain export --restore-only --type media --slug-prefix media/x/ --repo /path/to/brain
+```
+
+The `--restore-only` flag:
+
+- Resolves repoPath via the chain `--repo` → typed `sources.getDefault()` → hard error.
+  Never falls through to the current directory.
+- Only exports pages that match `db_only` patterns AND are missing from disk.
+- Ideal for container restart recovery and fresh clones.
+
+### 3. `gbrain storage status` — storage-tier health dashboard
+
+```bash
+# Human-readable status.
+gbrain storage status --repo /path/to/brain
+
+# JSON output for scripts and orchestrators.
+gbrain storage status --repo /path/to/brain --json
+```
+
+Output includes:
+
+- Total page counts by storage tier.
+- Disk usage breakdown by tier.
+- Missing files that need restoration (top 10 shown; full list in `--json`).
+- Configuration validation warnings.
+- Current tier directory listing.
+
+Example output:
+
+```
+Storage Status
+==============
+
+Repository: /data/brain
+Total pages: 15,243
+
+Storage Tiers:
+-------------
+DB tracked:     2,156 pages
+DB only:        12,887 pages
+Unspecified:    200 pages
+
+Disk Usage:
+-----------
+DB tracked:     45.2 MB
+DB only:        2.1 GB
+
+Missing Files (need restore):
+-----------------------------
+  media/x/tweet-1234567890
+  media/x/tweet-0987654321
+  ... and 47 more
+
+Use: gbrain export --restore-only --repo "/data/brain"
+
+Configuration:
+--------------
+DB tracked directories:
+  - people/
+  - companies/
+  - deals/
+
+DB-only directories:
+  - media/x/
+  - media/articles/
+  - meetings/transcripts/
+```
+
+## Validation
+
+`loadStorageConfig` runs `normalizeAndValidateStorageConfig` after parsing:
+
+- Auto-fixes (silent, with one-time info note showing what changed):
+  - Missing trailing `/` is added: `'media/x'` → `'media/x/'`.
+- Throws `StorageConfigError` (caller sees a clean exit-1 with actionable message):
+  - Same directory in both `db_tracked` and `db_only` (ambiguous routing).
+
+## Use cases
+
+### Brain repository scaling
+
+Perfect for brain repositories crossing 50K-200K+ files where:
+
+- Core knowledge (people, companies, deals) remains git-tracked.
+- Bulk data (tweets, articles, transcripts) moves to db_only.
+- Development stays fast with smaller git repos.
+- Full data remains available via the database.
+
+### Container-based deployments
+
+Essential for ephemeral container environments:
+
+- Git repo contains only essential files.
+- Container restarts don't lose db_only data.
+- `gbrain export --restore-only` quickly restores bulk files when needed.
+- Local disk acts as a cache layer.
+
+### Multi-environment consistency
+
+Enables consistent data access across environments:
+
+- Development: small git clone, restore bulk data on demand.
+- Production: full dataset via the database, selective local caching.
+- CI/CD: fast tests with git-tracked data only.
+
+## Migration strategy
+
+1. **Assess current repository**: use `gbrain storage status` to understand current distribution.
+2. **Plan directory structure**: identify which directories should be db_tracked vs db_only.
+3. **Create `gbrain.yml`**: add storage configuration to the repository root.
+4. **Test with dry-run**: `gbrain sync --dry-run` to verify behavior; `.gitignore` is NOT touched on dry-run.
+5. **Run a real sync**: `gbrain sync` updates `.gitignore` automatically on success.
+6. **Verify restore**: test `gbrain export --restore-only --repo .` against a small db_only directory.
+
+## Best practices
+
+- **Directory naming**: end storage paths with `/` (canonical form). The validator normalizes if you forget.
+- **Start small**: begin with clearly machine-generated directories in `db_only`.
+- **Address validation errors**: tier overlap is an error, not a warning. Fix it before sync.
+- **Test restore**: regularly test `--restore-only` in staging environments.
+- **Document decisions**: comment your `gbrain.yml` to explain tier choices.
+
+## PGLite engine note
+
+On the PGLite engine (gbrain's local-only embedded Postgres), the "DB" your db_only pages live in IS the local file gbrain uses for everything else. The `.gitignore` housekeeping still helps (keeps bulk content out of git history), but the offload-to-DB promise is technically vacuous. A once-per-process soft-warn explains when the engine is detected. To get full tiering, migrate to Postgres with `gbrain migrate --to supabase`.
+
+## Compatibility
+
+- **Backward compatible**: systems without `gbrain.yml` work unchanged.
+- **Progressive enhancement**: add configuration when needed.
+- **Database unchanged**: all data remains in Postgres regardless of tier.
+- **Existing workflows**: all existing `sync` and `export` behavior preserved.
+- **Deprecated keys**: `git_tracked` / `supabase_only` still load with a once-per-process warning.

gbrain.yml

@@ -0,0 +1,18 @@
+storage:
+  # Directories that are version-controlled — human-curated, edited by hand.
+  db_tracked:
+    - people/
+    - companies/
+    - deals/
+    - concepts/
+    - yc/
+    - ideas/
+    - projects/
+
+  # Directories persisted via the brain database only — bulk machine-generated
+  # content. .gitignored automatically by `gbrain sync`. Restorable from the DB
+  # via `gbrain export --restore-only`.
+  db_only:
+    - media/x/
+    - media/articles/
+    - meetings/transcripts/

llms-full.txt

@@ -104,15 +104,19 @@ strict behavior when unset.
 - `src/core/operations.ts` — Contract-first operation definitions (the foundation). Also exports upload validators: `validateUploadPath`, `validatePageSlug`, `validateFilename`. `OperationContext.remote` flags untrusted callers.
 - `src/core/engine.ts` — Pluggable engine interface (BrainEngine). `clampSearchLimit(limit, default, cap)` takes an explicit cap so per-operation caps can be tighter than `MAX_SEARCH_LIMIT`. Exports `LinkBatchInput` / `TimelineBatchInput` for the v0.12.1 bulk-insert API (`addLinksBatch` / `addTimelineEntriesBatch`). As of v0.13.1, `BrainEngine` has a `readonly kind: 'postgres' | 'pglite'` discriminator so migrations (`src/core/migrate.ts`) and other consumers can branch on engine without `instanceof` + dynamic imports.
 - `src/core/engine-factory.ts` — Engine factory with dynamic imports (`'pglite'` | `'postgres'`)
-- `src/core/pglite-engine.ts` — PGLite (embedded Postgres 17.5 via WASM) implementation, all 40 BrainEngine methods. `addLinksBatch` / `addTimelineEntriesBatch` use multi-row `unnest()` with manual `$N` placeholders. As of v0.13.1, `connect()` wraps `PGlite.create()` in a try/catch that emits an actionable error naming the macOS 26.3 WASM bug (#223) and pointing at `gbrain doctor`; the lock is released on failure so the next process can retry cleanly. v0.22.0: `searchKeyword` and `searchKeywordChunks` multiply `ts_rank` by the source-factor CASE expression at the chunk-grain level; `searchVector` becomes a two-stage CTE — inner CTE keeps `ORDER BY cc.embedding <=> vec` so HNSW stays usable, outer SELECT re-ranks by `raw_score * source_factor`. Inner LIMIT scales with offset to preserve pagination contract.
+- `src/core/pglite-engine.ts` — PGLite (embedded Postgres 17.5 via WASM) implementation, all 40 BrainEngine methods. `addLinksBatch` / `addTimelineEntriesBatch` use multi-row `unnest()` with manual `$N` placeholders. As of v0.13.1, `connect()` wraps `PGlite.create()` in a try/catch that emits an actionable error naming the macOS 26.3 WASM bug (#223) and pointing at `gbrain doctor`; the lock is released on failure so the next process can retry cleanly. v0.22.0: `searchKeyword` and `searchKeywordChunks` multiply `ts_rank` by the source-factor CASE expression at the chunk-grain level; `searchVector` becomes a two-stage CTE — inner CTE keeps `ORDER BY cc.embedding <=> vec` so HNSW stays usable, outer SELECT re-ranks by `raw_score * source_factor`. Inner LIMIT scales with offset to preserve pagination contract. As of v0.22.6.1, `initSchema()` calls `applyForwardReferenceBootstrap()` BEFORE replaying SCHEMA_SQL — probes for the specific forward-referenced state the embedded schema blob needs (`pages.source_id`, `links.link_source`, `links.origin_page_id`, `content_chunks.symbol_name`, `content_chunks.language`, `sources` FK target table) and adds only what's missing. Closes the upgrade-wedge bug class that bit users 10+ times across 6 schema versions over 2 years (#239/#243/#266/#357/#366/#374/#375/#378/#395/#396). No-op on fresh installs and modern brains.
 - `src/core/pglite-schema.ts` — PGLite-specific DDL (pgvector, pg_trgm, triggers)
-- `src/core/postgres-engine.ts` — Postgres + pgvector implementation (Supabase / self-hosted). `addLinksBatch` / `addTimelineEntriesBatch` use `INSERT ... SELECT FROM unnest($1::text[], ...) JOIN pages ON CONFLICT DO NOTHING RETURNING 1` — 4-5 array params regardless of batch size, sidesteps the 65535-parameter cap. As of v0.12.3, `searchKeyword` / `searchVector` scope `statement_timeout` via `sql.begin` + `SET LOCAL` so the GUC dies with the transaction instead of leaking across the pooled postgres.js connection (contributed by @garagon). `getEmbeddingsByChunkIds` uses `tryParseEmbedding` so one corrupt row skips+warns instead of killing the query. v0.22.0: `searchKeyword`, `searchKeywordChunks`, and `searchVector` apply source-aware ranking by inlining the source-factor CASE and `NOT (col LIKE …)` hard-exclude clause from `src/core/search/sql-ranking.ts`. `searchVector` switches to a two-stage CTE (HNSW-safe inner ORDER BY, source-boost re-rank in the outer SELECT) and carries `p.source_id` through inner→outer for v0.18 multi-source callers. v0.22.1 (#406): `_savedConfig` retains the connect config; `reconnect()` tears down + recreates the pool from saved config (called by supervisor watchdog after 3 consecutive health-check failures). `executeRaw` is a single-statement passthrough — no per-call retry (D3 dropped that as unsound for non-idempotent statements; recovery is supervisor-driven). v0.22.1 (#363, contributed by @orendi84): `connect()` applies `resolveSessionTimeouts()` from `db.ts` as connection-time startup parameters (`statement_timeout`, `idle_in_transaction_session_timeout`) so orphan pgbouncer backends can't hold locks for hours. v0.22.1 (#409, contributed by @atrevino47): `countStaleChunks()` + `listStaleChunks()` server-side-filter on `embedding IS NULL` for `embed --stale`, eliminating ~76 MB/call client-side pull on a fully-embedded brain; `upsertChunks()` resets both `embedding` AND `embedded_at` to NULL when chunk_text changes without a new embedding (consistency).
+- `src/core/postgres-engine.ts` — Postgres + pgvector implementation (Supabase / self-hosted). `addLinksBatch` / `addTimelineEntriesBatch` use `INSERT ... SELECT FROM unnest($1::text[], ...) JOIN pages ON CONFLICT DO NOTHING RETURNING 1` — 4-5 array params regardless of batch size, sidesteps the 65535-parameter cap. As of v0.12.3, `searchKeyword` / `searchVector` scope `statement_timeout` via `sql.begin` + `SET LOCAL` so the GUC dies with the transaction instead of leaking across the pooled postgres.js connection (contributed by @garagon). `getEmbeddingsByChunkIds` uses `tryParseEmbedding` so one corrupt row skips+warns instead of killing the query. v0.22.0: `searchKeyword`, `searchKeywordChunks`, and `searchVector` apply source-aware ranking by inlining the source-factor CASE and `NOT (col LIKE …)` hard-exclude clause from `src/core/search/sql-ranking.ts`. `searchVector` switches to a two-stage CTE (HNSW-safe inner ORDER BY, source-boost re-rank in the outer SELECT) and carries `p.source_id` through inner→outer for v0.18 multi-source callers. v0.22.1 (#406): `_savedConfig` retains the connect config; `reconnect()` tears down + recreates the pool from saved config (called by supervisor watchdog after 3 consecutive health-check failures). `executeRaw` is a single-statement passthrough — no per-call retry (D3 dropped that as unsound for non-idempotent statements; recovery is supervisor-driven). v0.22.1 (#363, contributed by @orendi84): `connect()` applies `resolveSessionTimeouts()` from `db.ts` as connection-time startup parameters (`statement_timeout`, `idle_in_transaction_session_timeout`) so orphan pgbouncer backends can't hold locks for hours. v0.22.1 (#409, contributed by @atrevino47): `countStaleChunks()` + `listStaleChunks()` server-side-filter on `embedding IS NULL` for `embed --stale`, eliminating ~76 MB/call client-side pull on a fully-embedded brain; `upsertChunks()` resets both `embedding` AND `embedded_at` to NULL when chunk_text changes without a new embedding (consistency). As of v0.22.6.1, `initSchema()` calls `applyForwardReferenceBootstrap()` BEFORE replaying SCHEMA_SQL on the same forward-reference probe set as the PGLite engine, so old Postgres brains pinned at v0.13/v0.18/v0.19 walk forward cleanly instead of wedging on `column "..." does not exist`.
 - `src/core/utils.ts` — Shared SQL utilities extracted from postgres-engine.ts. Exports `parseEmbedding(value)` (throws on unknown input, used by migration + ingest paths where data integrity matters) and as of v0.12.3 `tryParseEmbedding(value)` (returns `null` + warns once per process, used by search/rescore paths where availability matters more than strictness).
 - `src/core/db.ts` — Connection management, schema initialization. v0.22.1 (#363, contributed by @orendi84): `resolveSessionTimeouts()` returns `statement_timeout` + `idle_in_transaction_session_timeout` (defaults: 5min each, env-overridable via `GBRAIN_STATEMENT_TIMEOUT` / `GBRAIN_IDLE_TX_TIMEOUT` / `GBRAIN_CLIENT_CHECK_INTERVAL`). Both `connect()` (module singleton) and `PostgresEngine.connect()` (worker pool) consume the result via postgres.js's `connection` option, sending GUCs as startup parameters that survive PgBouncer transaction mode (unlike the prior `setSessionDefaults` post-pool SET, kept as a back-compat no-op shim).
 - `src/commands/migrate-engine.ts` — Bidirectional engine migration (`gbrain migrate --to supabase/pglite`)
 - `src/core/import-file.ts` — importFromFile + importFromContent (chunk + embed + tags)
-- `src/core/sync.ts` — Pure sync functions (manifest parsing, filtering, slug conversion)
+- `src/core/sync.ts` — Pure sync functions (manifest parsing, filtering, slug conversion). v0.22.12 (#500, foundation by @wintermute via #501): `classifyErrorCode(errorMsg)` regex-based classifier with 12 codes (`SLUG_MISMATCH`, `YAML_PARSE`, `YAML_DUPLICATE_KEY`, `MISSING_OPEN`, `MISSING_CLOSE`, `NESTED_QUOTES`, `EMPTY_FRONTMATTER`, `NULL_BYTES`, `INVALID_UTF8`, `STATEMENT_TIMEOUT`, `FILE_TOO_LARGE`, `SYMLINK_NOT_ALLOWED`) plus `UNKNOWN` fallback. `summarizeFailuresByCode(failures)` returns sorted `[{code, count}]`. `code?` optional field on `SyncFailure`; backfilled at ack time on pre-v0.22.12 entries. `acknowledgeSyncFailures()` returns `AcknowledgeResult { count, summary }`. Three regexes (`MISSING_OPEN`, `MISSING_CLOSE`, `EMPTY_FRONTMATTER`) broadened to match actual `markdown.ts:159-244` validator message strings, not just the literal code-name prefix. `FILE_TOO_LARGE` covers all three production size sites in `import-file.ts:199, 352, 401`; `SYMLINK_NOT_ALLOWED` covers the rejection at `:347`. Closes the silent-skip pattern that motivated #500.
 - `src/core/storage.ts` — Pluggable storage interface (S3, Supabase Storage, local)
+- `src/core/storage-config.ts` (v0.22.11) — Storage tiering: `loadStorageConfig` reads `gbrain.yml`, normalizes deprecated keys (`git_tracked` / `supabase_only`) to canonical (`db_tracked` / `db_only`) with once-per-process deprecation warning, and runs `normalizeAndValidateStorageConfig` (auto-fixes missing trailing `/`, throws `StorageConfigError` on tier overlap). Path-segment matcher: `media/x/` does NOT match `media/xerox/foo`. Replaces gray-matter (broken on delimiter-less YAML) with a dedicated parser for the `gbrain.yml` shape.
+- `src/core/disk-walk.ts` (v0.22.11) — `walkBrainRepo(repoPath)` returns `Map<slug, {size, mtimeMs}>` from one recursive `readdirSync`. Skips dot-dirs, `node_modules`, non-`.md` files. Used by `gbrain storage status` to replace per-page `existsSync + statSync` (~400K syscalls on 200K-page brains → tens).
+- `src/commands/storage.ts` (v0.22.11) — `gbrain storage status [--repo P] [--json]`. Split into pure data (`getStorageStatus`) + JSON formatter + human formatter (ASCII-only per D10) matching the `orphans.ts` pattern. `PageCountsByTier` and `DiskUsageByTier` are distinct nominal types so swaps fail at compile time.
+- `gbrain.yml` (brain repo root, v0.22.11) — Optional storage tiering config. Top-level `storage:` section with `db_tracked:` and `db_only:` array-valued keys. `gbrain sync` auto-manages `.gitignore` for `db_only` paths on successful sync (skips on dry-run, blocked-by-failures, submodule context, or `GBRAIN_NO_GITIGNORE=1`). `gbrain export --restore-only [--repo P] [--type T] [--slug-prefix S]` repopulates missing `db_only` files from the database.
 - `src/core/supabase-admin.ts` — Supabase admin API (project discovery, pgvector check)
 - `src/core/file-resolver.ts` — File resolution with fallback chain (local -> .redirect.yaml -> .redirect -> .supabase)
 - `src/core/chunkers/` — 3-tier chunking (recursive, semantic, LLM-guided). v0.19.0 adds `code.ts` — tree-sitter-based semantic chunker for 29 languages with embedded-asset WASMs (`src/assets/wasm/`), `@dqbd/tiktoken` cl100k_base tokenizer, small-sibling merging. `CHUNKER_VERSION` constant folded into `importCodeFile`'s `content_hash` so chunker shape changes force clean re-chunks across releases.
@@ -167,19 +171,26 @@ strict behavior when unset.
 - `src/core/minions/attachments.ts` — Attachment validation (path traversal, null byte, oversize, base64, duplicate detection)
 - `src/commands/agent.ts` (v0.16) — `gbrain agent run <prompt> [flags]` CLI. Submits `subagent` (or N children + 1 aggregator) under `{allowProtectedSubmit: true}`. Single-entry `--fanout-manifest` short-circuits. Children get `on_child_fail: 'continue'` + `max_stalled: 3`. `--follow` is the default on TTY; streams logs + polls `waitForCompletion` in parallel. Ctrl-C detaches, does not cancel.
 - `src/commands/agent-logs.ts` (v0.16) — `gbrain agent logs <job> [--follow] [--since]`. Merges JSONL heartbeat audit + `subagent_messages` into a chronological timeline. `parseSince` accepts ISO-8601 or relative (`5m`, `1h`, `2d`). Transcript tail renders only for terminal jobs.
-- `src/commands/jobs.ts` — `gbrain jobs` CLI subcommands + `gbrain jobs work` daemon. v0.13.1 surfaces the full `MinionJobInput` retry/backoff/timeout/idempotency surface as first-class CLI flags on `jobs submit`: `--max-stalled`, `--backoff-type fixed|exponential`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key`. `jobs smoke --sigkill-rescue` is the opt-in regression guard for #219. v0.16 wires `registerBuiltinHandlers` to always register `subagent` + `subagent_aggregator` (no env flag — `ANTHROPIC_API_KEY` is the natural cost gate, trust is via `PROTECTED_JOB_NAMES`) and loads `GBRAIN_PLUGIN_PATH` plugins at worker startup with a loud startup-line per plugin. `shell` handler still gated by `GBRAIN_ALLOW_SHELL_JOBS=1` (RCE surface, separate concern).
+- `src/commands/jobs.ts` — `gbrain jobs` CLI subcommands + `gbrain jobs work` daemon. v0.13.1 surfaces the full `MinionJobInput` retry/backoff/timeout/idempotency surface as first-class CLI flags on `jobs submit`: `--max-stalled`, `--backoff-type fixed|exponential`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key`. `jobs smoke --sigkill-rescue` is the opt-in regression guard for #219. v0.16 wires `registerBuiltinHandlers` to always register `subagent` + `subagent_aggregator` (no env flag — `ANTHROPIC_API_KEY` is the natural cost gate, trust is via `PROTECTED_JOB_NAMES`) and loads `GBRAIN_PLUGIN_PATH` plugins at worker startup with a loud startup-line per plugin. `shell` handler still gated by `GBRAIN_ALLOW_SHELL_JOBS=1` (RCE surface, separate concern). v0.22.10 (#521): the `autopilot-cycle` handler now forwards `job.data.phases` to `runCycle` (was previously discarded — caller-supplied phase selection silently became a full cycle). Phases are validated against `ALL_PHASES` from `src/core/cycle.ts`; invalid names are filtered out and an empty/missing array falls back to the default 6-phase cycle. v0.22.13 (PR #490 CODEX-1+CODEX-4): `sync` handler now resolves `sourceId` at entry by looking up `sources.local_path` (mirrors `cycle.ts:480`'s autopilot fix from PR #475) so multi-source brains read the per-source `last_commit` anchor instead of the global config key. Concurrency routed through the shared `autoConcurrency()` policy in `src/core/sync-concurrency.ts` instead of the prior hardcoded `4`; PGLite stays serial. `noEmbed` default is `true` (embed is a separate job — submit `gbrain embed --stale` after sync, or rely on the autopilot cycle's embed phase).
 - `src/commands/features.ts` — `gbrain features --json --auto-fix`: usage scan + feature adoption salesman
 - `src/commands/autopilot.ts` — `gbrain autopilot --install`: self-maintaining brain daemon (sync+extract+embed)
-- `src/mcp/server.ts` — MCP stdio server (generated from operations)
-- `src/commands/auth.ts` — Standalone token management (create/list/revoke/test)
+- `src/mcp/server.ts` — MCP stdio server (generated from operations). v0.22.7: tool-call handler delegates to `dispatchToolCall` from `src/mcp/dispatch.ts` so stdio + HTTP transports share one validation, context-build, and error-format path.
+- `src/mcp/dispatch.ts` (v0.22.7) — Shared tool-call dispatch consumed by both stdio (`server.ts`) and HTTP (`http-transport.ts`). Exports `dispatchToolCall(engine, name, params, opts)`, `buildOperationContext(engine, params, opts)`, and `validateParams(op, params)`. Single source of truth for `(ctx, params)` handler arg order and the 5-field `OperationContext` shape (engine + config + logger + dryRun + remote). Defaults to `remote: true` (untrusted); local CLI callers pass `remote: false`. Closed F1 (reversed handler args) + F2 (incomplete OperationContext) + F3 (no param validation) drift bugs in the original v0.22.5 HTTP transport.
+- `src/mcp/rate-limit.ts` (v0.22.7) — Bounded-LRU token-bucket limiter for `gbrain serve --http`. `buildDefaultLimiters()` returns the two-bucket pipeline used by http-transport: pre-auth IP (default 30/60s, fires BEFORE the DB lookup so brute-force load against `access_tokens` is actually capped) + post-auth token-id (default 60/60s). Tracks `lastTouchedMs` separately from `lastRefillMs` so an exhausted key can't be reset by hammering past the TTL. LRU cap (default 10K keys) bounds memory under attacker-controlled key growth; TTL prune at 2× window evicts abandoned buckets.
+- `src/mcp/http-transport.ts` (v0.22.7, rewrite) — `gbrain serve --http` HTTP transport. Postgres-only — fails fast at startup on PGLite (the `access_tokens` table only exists on Postgres). Bearer auth against SHA-256 hashes in `access_tokens`. CORS default-deny via `GBRAIN_HTTP_CORS_ORIGIN` allowlist. Body cap stream-counted (1 MiB default via `GBRAIN_HTTP_MAX_BODY_BYTES`) so chunked transfers without Content-Length still hit the cap. `last_used_at` SQL-level debounce (one UPDATE per token per 60s). Per-request audit row in `mcp_request_log` with token_name + operation + status + latency. Optional `GBRAIN_HTTP_TRUST_PROXY=1` honors `X-Forwarded-For` — only safe when bound to a private interface AND the proxy strips client-supplied XFF (otherwise enables IP spoofing past the pre-auth rate limit). `/health` does `SELECT 1` against Postgres and returns 503 + `status:unhealthy` when the DB is unreachable so orchestration doesn't see green pods while clients get misleading 401s. Replaces the standalone OAuth wrapper that was vulnerable to unauthenticated client registration.
+- `src/commands/auth.ts` — Token management for the HTTP transport. `gbrain auth create/list/revoke/test`. As of v0.22.7 wired into the main CLI (`src/cli.ts`); also runs standalone via `bun run src/commands/auth.ts ...` for environments without a compiled binary. Tokens stored as SHA-256 hashes in `access_tokens` (Postgres-only).
 - `src/commands/upgrade.ts` — Self-update CLI. `runPostUpgrade()` enumerates migrations from the TS registry (src/commands/migrations/index.ts) and tail-calls `runApplyMigrations(['--yes', '--non-interactive'])` so the mechanical side of every outstanding migration runs unconditionally.
 - `src/commands/migrations/` — TS migration registry (compiled into the binary; no filesystem walk of `skills/migrations/*.md` needed at runtime). `index.ts` lists migrations in semver order. `v0_11_0.ts` = Minions adoption orchestrator (8 phases). `v0_12_0.ts` = Knowledge Graph auto-wire orchestrator (5 phases: schema → config check → backfill links → backfill timeline → verify). `phaseASchema` has a 600s timeout (bumped from 60s in v0.12.1 for duplicate-heavy brains). `v0_12_2.ts` = JSONB double-encode repair orchestrator (4 phases: schema → repair-jsonb → verify → record). `v0_14_0.ts` = shell-jobs + autopilot cooperative (2 phases: schema ALTER minion_jobs.max_stalled SET DEFAULT 3 — superseded by v0.14.3's schema-level DEFAULT 5 + UPDATE backfill; pending-host-work ping for skills/migrations/v0.14.0.md). All orchestrators are idempotent and resumable from `partial` status. As of v0.14.2 (Bug 3), the RUNNER owns all ledger writes — orchestrators return `OrchestratorResult` and `apply-migrations.ts` persists a canonical `{version, status, phases}` shape after return. Orchestrators no longer call `appendCompletedMigration` directly. `statusForVersion` prefers `complete` over `partial` (never regresses). 3 consecutive partials → wedged → `--force-retry <version>` writes a `'retry'` reset marker. v0.14.3 (fix wave) ships schema-only migrations v14 (`pages_updated_at_index`) + v15 (`minion_jobs_max_stalled_default_5` with UPDATE backfill) via the `MIGRATIONS` array in `src/core/migrate.ts` — no orchestrator phases needed.
 - `src/commands/repair-jsonb.ts` — `gbrain repair-jsonb [--dry-run] [--json]`: rewrites `jsonb_typeof='string'` rows in place across 5 affected columns (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter). Fixes v0.12.0 double-encode bug on Postgres; PGLite no-ops. Idempotent.
 - `src/commands/orphans.ts` — `gbrain orphans [--json] [--count] [--include-pseudo]`: surfaces pages with zero inbound wikilinks, grouped by domain. Auto-generated/raw/pseudo pages filtered by default. Also exposed as `find_orphans` MCP operation. Shipped in v0.12.3 (contributed by @knee5).
-- `src/commands/doctor.ts` — `gbrain doctor [--json] [--fast] [--fix] [--dry-run] [--index-audit]`: health checks. v0.12.3 added `jsonb_integrity` + `markdown_body_completeness` reliability checks. v0.14.1: `--fix` delegates inlined cross-cutting rules to `> **Convention:** see [path](path).` callouts (pipes DRY violations into `src/core/dry-fix.ts`); `--fix --dry-run` previews without writing. v0.14.2: `schema_version` check fails loudly when `version=0` (migrations never ran — the #218 `bun install -g` signature) and routes users to `gbrain apply-migrations --yes`; new opt-in `--index-audit` flag (Postgres-only) reports zero-scan indexes from `pg_stat_user_indexes` (informational only, no auto-drop). v0.15.2: every DB check is wrapped in a progress phase; `markdown_body_completeness` runs under a 1s heartbeat timer so 10+ min scans are observable on 50K-page brains. v0.19.1 added `queue_health` (Postgres-only) with two subchecks: stalled-forever active jobs (started_at > 1h) and waiting-depth-per-name > threshold (default 10, override via `GBRAIN_QUEUE_WAITING_THRESHOLD`). Worker-heartbeat subcheck intentionally deferred to follow-up B7 because it needs a `minion_workers` table to produce ground-truth signal. Fix hints point at `gbrain repair-jsonb`, `gbrain sync --force`, `gbrain apply-migrations`, and `gbrain jobs get/cancel <id>`.
-- `src/core/migrate.ts` — schema-migration runner. Owns the `MIGRATIONS` array (source of truth for schema DDL). v0.14.2 extended the `Migration` interface with `sqlFor?: { postgres?, pglite? }` (engine-specific SQL overrides `sql`) and `transaction?: boolean` (set to false for `CREATE INDEX CONCURRENTLY`, which Postgres refuses inside a transaction; ignored on PGLite since it has no concurrent writers). Migration v14 (fix wave) uses a handler branching on `engine.kind` to run CONCURRENTLY on Postgres (with a pre-drop of any invalid remnant via `pg_index.indisvalid`) and plain `CREATE INDEX` on PGLite. v15 bumps `minion_jobs.max_stalled` default 1→5 and backfills existing non-terminal rows.
+- `src/commands/integrity.ts` — `gbrain integrity check|auto|review|extract`: bare-tweet detection, dead-link detection, three-bucket repair (auto-repair / review-queue / skip). `scanIntegrity()` is the shared library function called from `gbrain doctor` (sampled at limit=500) and `cmdCheck` (full scan). v0.22.8: batch-load fast path on Postgres uses `SELECT DISTINCT ON (slug)` in a single SQL query to fix the PgBouncer round-trip timeout (60s → ~6s) while preserving `engine.getAllSlugs()`'s `Set<string>` semantics on multi-source brains. Gated by `engine.kind === 'postgres'` at the call site so PGLite never enters batch; fallback `catch` logs at `GBRAIN_DEBUG=1` so real Postgres errors are diagnosable.
+- `src/commands/doctor.ts` — `gbrain doctor [--json] [--fast] [--fix] [--dry-run] [--index-audit]`: health checks. v0.12.3 added `jsonb_integrity` + `markdown_body_completeness` reliability checks. v0.14.1: `--fix` delegates inlined cross-cutting rules to `> **Convention:** see [path](path).` callouts (pipes DRY violations into `src/core/dry-fix.ts`); `--fix --dry-run` previews without writing. v0.14.2: `schema_version` check fails loudly when `version=0` (migrations never ran — the #218 `bun install -g` signature) and routes users to `gbrain apply-migrations --yes`; new opt-in `--index-audit` flag (Postgres-only) reports zero-scan indexes from `pg_stat_user_indexes` (informational only, no auto-drop). v0.15.2: every DB check is wrapped in a progress phase; `markdown_body_completeness` runs under a 1s heartbeat timer so 10+ min scans are observable on 50K-page brains. v0.19.1 added `queue_health` (Postgres-only) with two subchecks: stalled-forever active jobs (started_at > 1h) and waiting-depth-per-name > threshold (default 10, override via `GBRAIN_QUEUE_WAITING_THRESHOLD`). Worker-heartbeat subcheck intentionally deferred to follow-up B7 because it needs a `minion_workers` table to produce ground-truth signal. Fix hints point at `gbrain repair-jsonb`, `gbrain sync --force`, `gbrain apply-migrations`, and `gbrain jobs get/cancel <id>`. v0.22.12 (#500): `sync_failures` check shows `[CODE=N, ...]` breakdown for both unacked entries (warn) and acked-historical entries (ok), surfacing systemic failure modes (`SLUG_MISMATCH=2685`) instead of a bare count.
+- `src/core/migrate.ts` — schema-migration runner. Owns the `MIGRATIONS` array (source of truth for schema DDL). v0.14.2 extended the `Migration` interface with `sqlFor?: { postgres?, pglite? }` (engine-specific SQL overrides `sql`) and `transaction?: boolean` (set to false for `CREATE INDEX CONCURRENTLY`, which Postgres refuses inside a transaction; ignored on PGLite since it has no concurrent writers). Migration v14 (fix wave) uses a handler branching on `engine.kind` to run CONCURRENTLY on Postgres (with a pre-drop of any invalid remnant via `pg_index.indisvalid`) and plain `CREATE INDEX` on PGLite. v15 bumps `minion_jobs.max_stalled` default 1→5 and backfills existing non-terminal rows. v0.22.6.1: migration v24 (`rls_backfill_missing_tables`) uses `sqlFor: { pglite: '' }` to no-op on PGLite — PGLite has no RLS engine and is single-tenant by definition, and the v24 ALTERs target subagent tables that don't exist in pglite-schema.ts. Closes #395 (contributed by @jdcastro2).
 - `src/core/progress.ts` — Shared bulk-action progress reporter. Writes to stderr. Modes: `auto` (TTY: `\r`-rewriting; non-TTY: plain lines), `human`, `json` (JSONL), `quiet`. Rate-gated by `minIntervalMs` and `minItems`. `startHeartbeat(reporter, note)` helper for single long queries. `child()` composes phase paths. Singleton SIGINT/SIGTERM coordinator emits `abort` events for every live phase. EPIPE defense on both sync throws and stream `'error'` events. Zero dependencies. Introduced in v0.15.2.
 - `src/core/cli-options.ts` — Global CLI flag parser. `parseGlobalFlags(argv)` returns `{cliOpts, rest}` with `--quiet` / `--progress-json` / `--progress-interval=<ms>` stripped. `getCliOptions()` / `setCliOptions()` expose a module-level singleton so commands reach the resolved flags without parameter threading. `cliOptsToProgressOptions()` maps to reporter options. `childGlobalFlags()` returns the flag suffix to append to `execSync('gbrain ...')` calls in migration orchestrators. `OperationContext.cliOpts` extends shared-op dispatch for MCP callers.
+- `src/core/db-lock.ts` (v0.22.13) — generic `tryAcquireDbLock(engine, lockId, ttlMinutes)` over the existing `gbrain_cycle_locks` table. Parameterized lock id so different scopes can nest cleanly: `gbrain-cycle` for the broad cycle (held by `cycle.ts`) and `gbrain-sync` (`SYNC_LOCK_ID` constant) for `performSync`'s narrower writer window. Same UPSERT-with-TTL semantics as the prior cycle-only helper, just generalized. Survives PgBouncer transaction pooling (unlike session-scoped `pg_try_advisory_lock`); crashed holders auto-release once their TTL expires.
+- `src/core/sync-concurrency.ts` (v0.22.13) — single source of truth for the parallel-sync policy. Exports `autoConcurrency(engine, fileCount, override?)` (PGLite always serial; explicit override clamped to >=1; auto path returns `DEFAULT_PARALLEL_WORKERS=4` when `fileCount > AUTO_CONCURRENCY_FILE_THRESHOLD=100`), `shouldRunParallel(workers, fileCount, explicit)` (Q1: explicit `--workers` bypasses the >50-file floor), and `parseWorkers(s)` (rejects `'0'`, `'-3'`, `'foo'`, `'1.5'`, trailing chars — replaces the prior parseInt-with-no-validation in both `sync.ts` and `import.ts`). Used by `performSync`, `performFullSync`, `runImport`, and the Minion `sync` handler so the three sites can no longer drift.
+- `src/commands/sync.ts` — `gbrain sync` CLI + the `performSync` / `performFullSync` library entrypoints (consumed by the autopilot cycle and the Minion sync handler). v0.22.13 (PR #490): `performSync` wraps its body in a `gbrain-sync` writer lock so two concurrent syncs (manual + autopilot, two terminals, two Conductor workspaces) cannot both write `last_commit` and let the last writer win. Head-drift gate after the import phase re-checks `git rev-parse HEAD`; if HEAD moved (someone ran `git checkout` / `git pull` mid-sync), the bookmark refuses to advance. Vanished files now record a failedFiles entry instead of silent-skip — the silent-skip-then-advance pathology that survived prior hardening passes is dead. Worker engines wrap in try/finally so disconnect always fires (panic-path leak fix). Both PGLite-detection sites use `engine.kind === 'pglite'`. CLI accepts `--workers N` (alias `--concurrency N`), validated via `parseWorkers`. Explicit `--workers` bypasses the auto-path file-count floor; auto path defers to `autoConcurrency()`. Banner moved to stderr.
 - `src/core/cycle.ts` — v0.17 brain maintenance cycle primitive. `runCycle(engine: BrainEngine | null, opts: CycleOpts): Promise<CycleReport>` composes 6 phases in semantically-driven order (lint → backlinks → sync → extract → embed → orphans). Three callers: `gbrain dream` CLI, `gbrain autopilot` daemon's inline path, and the Minions `autopilot-cycle` handler (`src/commands/jobs.ts`). One source of truth for what the brain does overnight. Coordination via `gbrain_cycle_locks` DB table (TTL-based; works through PgBouncer transaction pooling, unlike session-scoped `pg_try_advisory_lock`) + `~/.gbrain/cycle.lock` file lock with PID-liveness for PGLite / engine=null mode. `CycleReport.schema_version: "1"` is the stable agent-consumable shape. `PhaseResult.error: { class, code, message, hint?, docs_url? }` is Stripe-API-tier structured failure info. `yieldBetweenPhases` hook awaited between every phase — Minions handler uses this to renew its job lock and prevent v0.14 stall-death regression. Engine nullable: filesystem phases (lint, backlinks) run without DB; DB phases skip with `status: "skipped", reason: "no_database"`. Lock-skip: read-only phase selections (`--phase orphans`) bypass the cycle lock. v0.22.1 (#403): `CycleOpts.signal?: AbortSignal` propagates the worker's abort signal; `checkAborted()` fires between every phase and throws if the signal is aborted (cooperative — can't interrupt a phase mid-execution). v0.22.1 (#417): `runPhaseSync` returns `pagesAffected` via `SyncPhaseResult`; `runCycle` captures it and threads to `runPhaseExtract` as the 4th arg, enabling incremental extract on the cycle path. v0.22.1 (Codex F2): `runPhaseSync` takes `willRunExtractPhase: boolean` and sets `noExtract: phases.includes('extract')` so `gbrain dream --phase sync` doesn't silently lose extraction. v0.22.5 (#475): new `resolveSourceForDir(engine, brainDir)` helper queries `SELECT id FROM sources WHERE local_path = $1 LIMIT 1`; `runPhaseSync` threads result as `sourceId` to `performSync()` so sync reads the per-source `sources.last_commit` anchor instead of the drift-prone global `config.sync.last_commit` key. Bare try/catch lets pre-v0.18 brains fall through to the global key. Closes the prod hang where every autopilot cycle ran a 30-min full reimport because the global anchor commit had been GC'd from git history.
 - `src/commands/dream.ts` — v0.17 `gbrain dream` CLI. ~80-line thin alias over `runCycle`. brainDir resolution requires explicit `--dir` OR `sync.repo_path` config (no more walk-up-cwd-for-.git footgun). Flags: `--dry-run`, `--json`, `--phase <name>`, `--pull`, `--dir <path>`. Exit code 1 on status=failed (partial/warn not fatal — don't page on warnings).
 - `scripts/check-progress-to-stdout.sh` — CI guard against regressing to `\r`-on-stdout progress. Wired into `bun run test` via `scripts/check-progress-to-stdout.sh && bun test` in package.json.
@@ -291,6 +302,10 @@ Key commands added in v0.14.3 (fix wave):
 - `gbrain jobs submit` gains `--max-stalled`, `--backoff-type`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key` — exposing existing `MinionJobInput` fields as first-class CLI flags.
 - `gbrain jobs smoke --sigkill-rescue` — opt-in regression smoke case simulating a killed worker; asserts the v0.14.3 schema default (`max_stalled=5`) actually rescues on first stall.
 
+Key commands added in v0.22.13 (PR #490):
+- `gbrain sync --workers N` (alias `--concurrency N`) — parallelize the import phase using per-worker Postgres engines (small pool of 2 each) with an atomic queue index. Auto-concurrency: defaults to 4 workers when the diff exceeds 100 files. Smaller diffs stay serial. Explicit `--workers` always wins (even on a 30-file diff). PGLite forces serial regardless. Validation rejects `0`, negatives, non-integers loud (replaces the prior silent fall-through to auto-concurrency).
+- `gbrain import --workers N` — same `parseWorkers()` validation as sync; same try/finally worker-engine cleanup. Behavior surface unchanged.
+
 ## Testing
 
 `bun test` runs all tests. After the v0.12.1 release: ~75 unit test files + 8 E2E test files (1412 unit pass, 119 E2E when `DATABASE_URL` is set — skip gracefully otherwise). Unit tests run
@@ -302,7 +317,9 @@ parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redac
 `test/files.test.ts` (MIME/hash), `test/import-file.test.ts` (import pipeline),
 `test/upgrade.test.ts` (schema migrations),
 `test/file-migration.test.ts` (file migration), `test/file-resolver.test.ts` (file resolution),
-`test/import-resume.test.ts` (import checkpoints), `test/migrate.test.ts` (migration; v8/v9 helper-btree-index SQL structural assertions + 1000-row wall-clock fixtures that guard the O(n²)→O(n log n) fix + v0.13.1 assertions on v12/v13 SQL shape, `sqlFor` + `transaction:false` runner semantics, and the `max_stalled DEFAULT 1` regression guard),
+`test/import-resume.test.ts` (import checkpoints), `test/migrate.test.ts` (migration; v8/v9 helper-btree-index SQL structural assertions + 1000-row wall-clock fixtures that guard the O(n²)→O(n log n) fix + v0.13.1 assertions on v12/v13 SQL shape, `sqlFor` + `transaction:false` runner semantics, the `max_stalled DEFAULT 1` regression guard, and v0.22.6.1 v24 `sqlFor.pglite: ''` no-op assertion),
+`test/bootstrap.test.ts` (v0.22.6.1 — bootstrap contract: no-op on fresh install, idempotent across two `initSchema()` calls, no-op on modern brain that already has every probed column, full bootstrap path on simulated pre-v0.18 brain, fresh-install regression guard, pre-v0.13 `links` shape coverage),
+`test/schema-bootstrap-coverage.test.ts` (v0.22.6.1 CI guard — `REQUIRED_BOOTSTRAP_COVERAGE` lists every forward reference in PGLITE_SCHEMA_SQL; the test fails loudly if `applyForwardReferenceBootstrap` skips one. When you add a column-with-index to the embedded schema blob, you extend both arrays or this guard fails. The pattern that broke gbrain ten times in two years is now structurally prevented.),
 `test/setup-branching.test.ts` (setup flow), `test/slug-validation.test.ts` (slug validation),
 `test/storage.test.ts` (storage backends), `test/supabase-admin.test.ts` (Supabase admin),
 `test/yaml-lite.test.ts` (YAML parsing), `test/check-update.test.ts` (version check + update CLI),
@@ -344,6 +361,9 @@ parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redac
 `test/orphans.test.ts` (v0.12.3 orphans command: detection, pseudo filtering, text/json/count outputs, MCP op),
 `test/postgres-engine.test.ts` (v0.12.3 statement_timeout scoping: `sql.begin` + `SET LOCAL` shape, source-level grep guardrail against reintroduced bare `SET statement_timeout`),
 `test/sync.test.ts` (sync logic + v0.12.3 regression guard asserting top-level `engine.transaction` is not called),
+`test/sync-concurrency.test.ts` (v0.22.13 PR #490: 17 cases covering `autoConcurrency()` thresholds + PGLite-forces-serial + explicit-override clamping, `shouldRunParallel()` Q1 explicit-bypasses-floor contract, and `parseWorkers()` validation that rejects `'0'`/`'-3'`/`'foo'`/`'1.5'`/trailing chars),
+`test/sync-parallel.test.ts` (v0.22.13 PR #490: PGLite-routed coverage of the bookmark gate under concurrency request, head-drift gate, vanished-file failure capture, PGLite-stays-serial, and the `gbrain-sync` writer-lock contract — 7 cases),
+`test/sync-failures.test.ts` (v0.22.12: 28 cases pinning `classifyErrorCode` regex coverage for all 12 codes against literal production message strings from `markdown.ts:159-244` and `import-file.ts:199, 347, 352, 401`; `summarizeFailuresByCode` sort + pre-classified-honor; `recordSyncFailures` code-field persistence; `acknowledgeSyncFailures` AcknowledgeResult shape + backfill on pre-v0.22.12 entries),
 `test/doctor.test.ts` (doctor command + v0.12.3 assertions that `jsonb_integrity` scans the four v0.12.0 write sites and `markdown_body_completeness` is present),
 `test/utils.test.ts` (shared SQL utilities + `tryParseEmbedding` null-return and single-warn semantics),
 `test/build-llms.test.ts` (llms.txt/llms-full.txt generator: path resolution, idempotence, spec shape, regen-drift guard, content contract, AGENTS.md install-path mirror, size-budget enforcement — 7 cases),
@@ -354,20 +374,26 @@ parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redac
 `test/skill-manifest.test.ts` (v0.19 skill manifest parser: drift detection, managed-block markers),
 `test/skillify-scaffold.test.ts` (v0.19 `gbrain skillify scaffold` stubs: SKILL.md, script, tests, routing-eval fixtures),
 `test/skillpack-install.test.ts` (v0.19 `gbrain skillpack install` managed-block install / update / no-clobber semantics),
-`test/skillpack-sync-guard.test.ts` (v0.19 sync-guard: bundled skills stay byte-identical to `skills/` source).
+`test/skillpack-sync-guard.test.ts` (v0.19 sync-guard: bundled skills stay byte-identical to `skills/` source),
+`test/http-transport.test.ts` (v0.22.7 HTTP transport: 23 unit cases covering bearer auth + missing/no-Bearer/unknown/revoked + `/health` bypass, F1+F2 round-trip via dispatch.ts, F3 invalid_params, application/json response shape (not SSE), CORS default-deny + allowlist, body cap on Content-Length AND chunked, two-bucket rate limit (refill, exhaust+Retry-After, LRU eviction, TTL prune, pre-auth IP fires before DB), and `mcp_request_log` audit on success + auth_failed).
 
 E2E tests (`test/e2e/`): Run against real Postgres+pgvector. Require `DATABASE_URL`.
 - `bun run test:e2e` runs Tier 1 (mechanical, all operations, no API keys). Includes 9 dedicated cases for the postgres-engine `addLinksBatch` / `addTimelineEntriesBatch` bind path — postgres-js's `unnest()` binding is structurally different from PGLite's and gets its own coverage.
 - `test/e2e/search-quality.test.ts` runs search quality E2E against PGLite (no API keys, in-memory)
 - `test/e2e/graph-quality.test.ts` runs the v0.10.3 knowledge graph pipeline (auto-link via put_page, reconciliation, traversePaths) against PGLite in-memory
 - `test/e2e/postgres-jsonb.test.ts` — v0.12.2 regression test. Round-trips all 5 JSONB write sites (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter) against real Postgres and asserts `jsonb_typeof='object'` plus `->>'key'` returns the expected scalar. The test that should have caught the original double-encode bug.
+- `test/e2e/integrity-batch.test.ts` (v0.22.8) — parity tests for `scanIntegrity`'s batch-load fast path vs sequential. Four cases (dedup, hits, validate, topPages) seed a fixture and assert both paths return identical results. Dedup case uses raw SQL via `getConn().unsafe()` to seed a `(test-source-2, people/alice)` row alongside the default-source row, since `engine.putPage` doesn't take a `source_id`. Pins the codex-caught multi-source overcounting regression.
 - `test/e2e/jsonb-roundtrip.test.ts` — v0.12.3 companion regression against the 4 doctor-scanned JSONB sites. Assertion-level overlap with `postgres-jsonb.test.ts` is intentional defense-in-depth: if doctor's scan surface ever drifts from the actual write surface, one of these tests catches it.
+- `test/e2e/sync.test.ts` (v0.22.12 — `--skip-failed` failure-loop test, alongside the existing 13 happy-path tests): exercises the full chain — broken file → `performSync` returns `blocked_by_failures` with grouped breakdown → `performSync({skipFailed: true})` advances bookmark and returns `AcknowledgeResult` with code summary → second broken file → second cycle. Saves and restores the user's real `~/.gbrain/sync-failures.jsonl` so the test is hermetic on a developer machine. Asserts bookmark gating, JSONL state, dedup across paths, summary aggregation, and the literal doctor-rendering string format. This is the integration test that proves the v0.22.12 chain holds together — unit tests cover the pure functions in isolation, this covers the integration.
 - `test/e2e/upgrade.test.ts` runs check-update E2E against real GitHub API (network required)
 - `test/e2e/minions-shell-pglite.test.ts` (v0.20.4) exercises the PGLite `--follow` inline shell-job path (in-memory, no `DATABASE_URL` required) — the path the consolidated minion-orchestrator skill documents for dev use
 - `test/e2e/openclaw-reference-compat.test.ts` (v0.19) — exercises `check-resolvable` + `skillpack install` against a minimal AGENTS.md workspace fixture (`test/fixtures/openclaw-reference-minimal/`), regression guard for the 107-skill OpenClaw deployment shape
 - `test/e2e/search-swamp.test.ts` (v0.22.0) — reproduces the headline source-swamp case. Seeds a curated `originals/talks/article-outline-fat-code` page against two `wintermute/chat/` pages stuffed with the same multi-word phrase. Asserts the article wins keyword AND vector ranking, that `detail=high` lets the chat swamp re-surface (temporal-query workflow preserved), and that `source_id` passes through the two-stage CTE intact. PGLite in-memory.
 - `test/e2e/search-exclude.test.ts` (v0.22.0) — verifies `test/` + `archive/` pages are hidden by default, that `include_slug_prefixes` opts back in, and that caller-supplied `exclude_slug_prefixes` adds to defaults. Both keyword and vector search paths covered.
 - `test/e2e/engine-parity.test.ts` (v0.22.0) — Postgres ↔ PGLite top-result and result-set parity for `searchKeyword` + `searchVector`. Codex flagged that Postgres ranks pages then picks best chunk while PGLite returns chunks directly — without parity coverage the source-boost fix could pass on PGLite and fail on Postgres. Skips gracefully when `DATABASE_URL` is unset.
+- `test/e2e/postgres-bootstrap.test.ts` (v0.22.6.1) — exercises `PostgresEngine.initSchema()` directly against a fresh real Postgres database. Asserts the bootstrap path is no-op on fresh installs and that SCHEMA_SQL replays cleanly through the engine path (not via the standalone `db.initSchema` from `src/core/db.ts`, which would have produced false-positive coverage). Codex caught the E2E-shape gap during plan review.
+- `test/e2e/http-transport.test.ts` (v0.22.7) — 8 cases against real Postgres covering `gbrain serve --http` end-to-end: bearer auth round-trip, `last_used_at` SQL-level debounce semantics, `mcp_request_log` row insertion on success and auth_failed paths, `/health` DB-down → 503 (DB-probing health check), and the F1+F2+F3 dispatch round-trip with a real operation. Skips gracefully when `DATABASE_URL` is unset.
+- `test/e2e/sync-parallel.test.ts` (v0.22.13 PR #490) — DATABASE_URL-gated. T2: 60-file Postgres sync at concurrency=4 imports all + no connection leak (probes `pg_stat_activity` before/after to confirm worker engines disconnected). P4: 120-file serial-vs-parallel benchmark prints `SYNC_PARALLEL_BENCH N files | serial=Xms | parallel(4)=Yms | speedup=Zx` for CHANGELOG quoting. Asserts parallel ≤ serial × 1.5 (CI-noise tolerant; not a strict speedup gate).
 - Tier 2 (`skills.test.ts`) requires OpenClaw + API keys, runs nightly in CI
 - If `.env.testing` doesn't exist in this directory, check sibling worktrees for one:
   `find ../  -maxdepth 2 -name .env.testing -print -quit` and copy it here if found.
@@ -1348,12 +1374,13 @@ Add to `~/.claude/server.json` (Claude Code), Settings > MCP Servers (Cursor), o
 ### Remote MCP (Claude Desktop, Cowork, Perplexity)
 
 ```bash
-ngrok http 8787 --url your-brain.ngrok.app
-bun run src/commands/auth.ts create "claude-desktop"
+gbrain auth create "claude-desktop"            # tokens via the existing CLI
+gbrain serve --http --port 8787                 # built-in HTTP transport (Postgres-only)
+ngrok http 8787 --url your-brain.ngrok.app      # any tunnel works
 claude mcp add gbrain -t http https://your-brain.ngrok.app/mcp -H "Authorization: Bearer TOKEN"
 ```
 
-Per-client guides: [`docs/mcp/`](docs/mcp/DEPLOY.md). ChatGPT requires OAuth 2.1 (not yet implemented).
+Per-client guides: [`docs/mcp/`](docs/mcp/DEPLOY.md). Hardening defaults, env vars, and threat model: [SECURITY.md](SECURITY.md). ChatGPT requires OAuth 2.1 (not yet implemented).
 
 ### Using gbrain with GStack
 
@@ -1627,6 +1654,30 @@ accumulate rows across separate single-skill installs instead of overwriting eac
 Read [`skills/skillify/SKILL.md`](skills/skillify/SKILL.md) for the full 10-item checklist
 and the anti-patterns it catches.
 
+## Storage tiering: keep bulk content out of git (v0.22.11)
+
+When your brain crosses 100K files and bulk machine-generated content (tweets, articles, transcripts)
+becomes the size driver, declare which directories belong in git and which live in the database only.
+
+```yaml
+# gbrain.yml at the brain repo root
+storage:
+  db_tracked:
+    - people/
+    - companies/
+    - deals/
+  db_only:
+    - media/x/
+    - media/articles/
+    - meetings/transcripts/
+```
+
+`gbrain sync` auto-manages your `.gitignore` for `db_only` paths. `gbrain export --restore-only --repo .`
+repopulates missing files from the database (container restart, fresh clone, accidental rm).
+`gbrain storage status` shows the tier breakdown.
+
+Full guide: [docs/storage-tiering.md](docs/storage-tiering.md).
+
 ## Getting Data In
 
 GBrain ships integration recipes that your agent sets up for you. Each recipe tells the agent what credentials to ask for, how to validate, and what cron to register.
@@ -1882,8 +1933,11 @@ SEARCH
   gbrain query <question>              Hybrid search (vector + keyword + RRF)
 
 IMPORT
-  gbrain import <dir> [--no-embed]      Import markdown (idempotent)
-  gbrain sync [--repo <path>]           Git-to-brain incremental sync
+  gbrain import <dir> [--no-embed] [--workers N]
+                                        Import markdown (idempotent)
+  gbrain sync [--repo <path>] [--workers N]
+                                        Git-to-brain incremental sync
+                                        (>100-file diffs auto-parallelize 4 workers on Postgres)
   gbrain export [--dir ./out/]          Export to markdown
 
 FILES
@@ -1925,6 +1979,8 @@ ADMIN
   gbrain doctor --locks                 List idle-in-tx backends (57014 diagnostic, Postgres only)
   gbrain stats                          Brain statistics
   gbrain serve                          MCP server (stdio)
+  gbrain serve --http --port 8787       MCP server (HTTP, Postgres-only, bearer auth)
+  gbrain auth create|list|revoke|test   Token management for the HTTP transport
   gbrain integrations                   Integration recipe dashboard
   gbrain sources list|add|remove|...    Multi-source brain management (v0.18)
   gbrain dream [--dry-run] [--phase N]  One maintenance cycle then exit (cron-friendly)
@@ -4105,9 +4161,14 @@ Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/mcp/DEPLOY
 
 # Deploy GBrain Remote MCP Server
 
+> **v0.22.7+:** Use `gbrain serve --http` for remote access. It includes built-in
+> bearer token auth, default-deny CORS, two-bucket rate limiting, body cap, and
+> per-request audit log. **Postgres-only** (PGLite is local-only by design).
+> See [SECURITY.md](../../SECURITY.md) for env vars and tunable defaults.
+
 Access your brain from any device, any AI client. GBrain's MCP server runs locally
-via `gbrain serve` (stdio). For remote access, wrap it in an HTTP server behind a
-public tunnel.
+via `gbrain serve` (stdio). For remote access, expose it via the built-in HTTP
+transport behind a public tunnel.
 
 ## Two Paths
 
@@ -4118,21 +4179,23 @@ gbrain serve
 ```
 
 Works with Claude Code, Cursor, Windsurf, and any MCP client that supports stdio.
-No server, no tunnel, no token needed.
+No server, no tunnel, no token needed. Works on both PGLite and Postgres engines.
 
-### Remote (any device, any AI client)
+### Remote (any device, any AI client) — Postgres only
 
 ```
 Your AI client (Claude Desktop, Perplexity, etc.)
   → ngrok tunnel (https://YOUR-DOMAIN.ngrok.app)
-  → Your HTTP server (wraps gbrain serve)
-  → Supabase Postgres (via pooler connection string)
+  → gbrain serve --http  (built-in transport with bearer auth)
+  → Postgres (pooler connection or self-hosted)
 ```
 
 This requires:
-1. A machine running `gbrain serve` behind an HTTP wrapper
-2. A public tunnel (ngrok, Tailscale, or cloud host)
-3. Bearer token auth for security
+1. A Postgres-backed brain (the `access_tokens` table only exists on Postgres;
+   running `gbrain serve --http` against a PGLite install fails fast at startup)
+2. A machine running `gbrain serve --http`
+3. A public tunnel (ngrok, Tailscale, or cloud host)
+4. A bearer token created via `gbrain auth create <name>`
 
 ## Remote Setup
 
@@ -4151,13 +4214,13 @@ ngrok http 8787 --url your-brain.ngrok.app  # Hobby tier for fixed domain
 
 ```bash
 # Create a token for each client
-bun run src/commands/auth.ts create "claude-desktop"
+gbrain auth create "claude-desktop"
 
 # List all tokens
-bun run src/commands/auth.ts list
+gbrain auth list
 
 # Revoke a token
-bun run src/commands/auth.ts revoke "claude-desktop"
+gbrain auth revoke "claude-desktop"
 ```
 
 Tokens are per-client. Create one for each device/app. Revoke individually
@@ -4173,7 +4236,7 @@ if compromised. Tokens are stored SHA-256 hashed in your database.
 ### 4. Verify
 
 ```bash
-bun run src/commands/auth.ts test \
+gbrain auth test \
   https://YOUR-DOMAIN.ngrok.app/mcp \
   --token YOUR_TOKEN
 ```
@@ -4201,7 +4264,7 @@ Funnel, and cloud hosts (Fly.io, Railway).
 Include the Authorization header: `Authorization: Bearer YOUR_TOKEN`
 
 **"invalid_token" error**
-Run `bun run src/commands/auth.ts list` to see active tokens.
+Run `gbrain auth list` to see active tokens.
 
 **"service_unavailable" error**
 Database connection failed. Check your Supabase dashboard for outages.

package.json

@@ -1,6 +1,6 @@
 {
   "name": "gbrain",
-  "version": "0.22.6",
+  "version": "0.22.13",
   "description": "Postgres-native personal knowledge brain with hybrid RAG search",
   "type": "module",
   "main": "src/core/index.ts",
@@ -32,8 +32,9 @@
     "build:all": "bun build --compile --target=bun-darwin-arm64 --outfile bin/gbrain-darwin-arm64 src/cli.ts && bun build --compile --target=bun-linux-x64 --outfile bin/gbrain-linux-x64 src/cli.ts",
     "build:schema": "bash scripts/build-schema.sh",
     "build:llms": "bun run scripts/build-llms.ts",
-    "test": "scripts/check-jsonb-pattern.sh && scripts/check-progress-to-stdout.sh && scripts/check-wasm-embedded.sh && bun run typecheck && bun test --timeout=60000",
+    "test": "scripts/check-jsonb-pattern.sh && scripts/check-progress-to-stdout.sh && scripts/check-trailing-newline.sh && scripts/check-wasm-embedded.sh && bun run typecheck && bun test --timeout=60000",
     "check:wasm": "scripts/check-wasm-embedded.sh",
+    "check:newlines": "scripts/check-trailing-newline.sh",
     "test:e2e": "bash scripts/run-e2e.sh",
     "typecheck": "tsc --noEmit",
     "check:jsonb": "scripts/check-jsonb-pattern.sh",
@@ -63,6 +64,7 @@
   },
   "devDependencies": {
     "@types/bun": "latest",
+    "bun-types": "^1.3.13",
     "typescript": "^5.6.0"
   },
   "trustedDependencies": [

scripts/check-trailing-newline.sh

@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+# CI guard: every text file under src/, test/, and the repo root .yml/.md
+# files must end with a newline. POSIX-noncompliant trailing data shows up
+# as a phantom diff on every future edit and trips most linters.
+#
+# Sibling to scripts/check-progress-to-stdout.sh and
+# scripts/check-jsonb-pattern.sh per CLAUDE.md's CI guard pattern.
+# Wired into `bun run test` via package.json's `test` script.
+
+set -euo pipefail
+
+# Files to check: anything tracked under src/ + test/ that's a code/text file.
+# Also the top-level *.yml + *.md the repo controls. Portable to bash 3.2
+# (macOS default) — no mapfile, no associative arrays.
+files=$(
+  git ls-files \
+    'src/**/*.ts' 'src/**/*.js' 'src/**/*.json' 'src/**/*.sql' 'src/**/*.md' \
+    'test/**/*.ts' 'test/**/*.js' 'test/**/*.json' 'test/**/*.md' \
+    'gbrain.yml' '*.md' \
+  2>/dev/null | sort -u
+)
+
+missing=""
+total=0
+while IFS= read -r f; do
+  [ -n "$f" ] || continue
+  [ -f "$f" ] || continue
+  [ -s "$f" ] || continue
+  total=$((total + 1))
+  if [ -n "$(tail -c 1 "$f")" ]; then
+    missing="${missing}  $f"$'\n'
+  fi
+done <<< "$files"
+
+if [ -n "$missing" ]; then
+  echo "ERROR: the following files are missing a trailing newline:" >&2
+  printf '%s' "$missing" >&2
+  echo >&2
+  echo "Fix: append a newline. e.g. \`printf '\\n' >> <file>\` or your editor's" >&2
+  echo "'final newline' setting (most editors do this automatically)." >&2
+  exit 1
+fi
+
+echo "trailing-newline check: ok ($total files)"

scripts/test-shard.sh

@@ -0,0 +1,76 @@
+#!/usr/bin/env bash
+# Partition unit test files into N shards by stable hash and run one shard.
+#
+# Usage: scripts/test-shard.sh <shard-index> <total-shards>
+#   shard-index: 1-based (1..N)
+#   total-shards: positive integer
+#
+# E2E tests under test/e2e/ are excluded — they need DATABASE_URL and run via
+# bun run test:e2e separately.
+#
+# Stable partitioning: a file's shard is `(hash(path) % N) + 1`. Same file
+# lands in the same shard on every run, regardless of how many other files
+# exist, so retries are reproducible. Hash is FNV-1a — pure shell, no jq.
+set -euo pipefail
+
+if [ "$#" -ne 2 ]; then
+  echo "usage: scripts/test-shard.sh <shard-index> <total-shards>" >&2
+  exit 1
+fi
+
+SHARD_INDEX="$1"
+TOTAL_SHARDS="$2"
+
+if ! [[ "$SHARD_INDEX" =~ ^[0-9]+$ ]] || ! [[ "$TOTAL_SHARDS" =~ ^[0-9]+$ ]]; then
+  echo "error: shard index and total must be positive integers" >&2
+  exit 1
+fi
+if [ "$SHARD_INDEX" -lt 1 ] || [ "$SHARD_INDEX" -gt "$TOTAL_SHARDS" ]; then
+  echo "error: shard index $SHARD_INDEX out of range 1..$TOTAL_SHARDS" >&2
+  exit 1
+fi
+
+cd "$(dirname "$0")/.."
+
+# Find all unit test files, deterministic order. Excludes test/e2e/.
+# Portable: avoid `mapfile` (bash 4+) so this runs on macOS bash 3.2 too.
+FILES=()
+while IFS= read -r line; do
+  FILES+=("$line")
+done < <(find test -name '*.test.ts' -not -path 'test/e2e/*' | sort)
+
+if [ "${#FILES[@]}" -eq 0 ]; then
+  echo "no test files found under test/" >&2
+  exit 1
+fi
+
+# FNV-1a 32-bit hash of a string — implemented in pure bash so we don't depend
+# on python/openssl/etc on the runner. Output is decimal.
+fnv1a() {
+  local str="$1"
+  local h=2166136261  # FNV offset basis
+  local i ord
+  for (( i=0; i<${#str}; i++ )); do
+    ord=$(printf '%d' "'${str:$i:1}")
+    h=$(( (h ^ ord) & 0xFFFFFFFF ))
+    h=$(( (h * 16777619) & 0xFFFFFFFF ))
+  done
+  echo "$h"
+}
+
+SHARD_FILES=()
+for f in "${FILES[@]}"; do
+  hash=$(fnv1a "$f")
+  bucket=$(( hash % TOTAL_SHARDS + 1 ))
+  if [ "$bucket" -eq "$SHARD_INDEX" ]; then
+    SHARD_FILES+=("$f")
+  fi
+done
+
+echo "shard $SHARD_INDEX/$TOTAL_SHARDS: ${#SHARD_FILES[@]}/${#FILES[@]} files"
+if [ "${#SHARD_FILES[@]}" -eq 0 ]; then
+  echo "warning: shard $SHARD_INDEX has no files (rehash or reduce shard count)" >&2
+  exit 0
+fi
+
+exec bun test --timeout=60000 "${SHARD_FILES[@]}"

src/cli.ts

@@ -19,7 +19,7 @@ for (const op of operations) {
 }
 
 // CLI-only commands that bypass the operation layer
-const CLI_ONLY = new Set(['init', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'repos', 'code-def', 'code-refs', 'reindex-code', 'code-callers', 'code-callees', 'frontmatter']);
+const CLI_ONLY = new Set(['init', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'storage', 'repos', 'code-def', 'code-refs', 'reindex-code', 'code-callers', 'code-callees', 'frontmatter', 'auth']);
 
 async function main() {
   // Parse global flags (--quiet / --progress-json / --progress-interval)
@@ -285,6 +285,11 @@ async function handleCliOnly(command: string, args: string[]) {
     await runIntegrations(args);
     return;
   }
+  if (command === 'auth') {
+    const { runAuth } = await import('./commands/auth.ts');
+    await runAuth(args);
+    return;
+  }
   if (command === 'resolvers') {
     const { runResolvers } = await import('./commands/resolvers.ts');
     await runResolvers(args);
@@ -447,7 +452,7 @@ async function handleCliOnly(command: string, args: string[]) {
       }
       case 'serve': {
         const { runServe } = await import('./commands/serve.ts');
-        await runServe(engine);
+        await runServe(engine, args);
         return; // serve doesn't disconnect
       }
       case 'call': {
@@ -525,6 +530,11 @@ async function handleCliOnly(command: string, args: string[]) {
         await runSources(engine, args);
         break;
       }
+      case 'storage': {
+        const { runStorage } = await import('./commands/storage.ts');
+        await runStorage(engine, args);
+        break;
+      }
       case 'code-def': {
         const { runCodeDef } = await import('./commands/code-def.ts');
         await runCodeDef(engine, args);
@@ -640,6 +650,8 @@ IMPORT/EXPORT
   sync --watch [--interval N]        Continuous sync (loops until stopped)
   sync --install-cron                Install persistent sync daemon
   export [--dir ./out/]              Export to markdown
+  export --restore-only [--repo <p>] Restore missing supabase-only files
+        [--type T] [--slug-prefix S] With optional filters
 
 FILES
   files list [slug]                  List stored files
@@ -721,6 +733,8 @@ ADMIN
   features [--json] [--auto-fix]     Scan usage + recommend unused features
   autopilot [--repo] [--interval N]  Self-maintaining brain daemon
   config [show|get|set] <key> [val]  Brain config
+  storage status [--repo <path>]     Storage tier status and health
+        [--json]                     (git-tracked vs supabase-only)
   serve                              MCP server (stdio)
   call <tool> '<json>'               Raw tool invocation
   version                            Version info

src/commands/auth.ts

@@ -1,20 +1,29 @@
 #!/usr/bin/env bun
 /**
- * GBrain token management — standalone script, no gbrain CLI dependency.
+ * GBrain token management.
  *
- * Usage:
+ * Wired into the CLI as of v0.22.5:
+ *   gbrain auth create "claude-desktop"
+ *   gbrain auth list
+ *   gbrain auth revoke "claude-desktop"
+ *   gbrain auth test <url> --token <token>
+ *
+ * Also runs standalone (no compiled binary required):
  *   DATABASE_URL=... bun run src/commands/auth.ts create "claude-desktop"
- *   DATABASE_URL=... bun run src/commands/auth.ts list
- *   DATABASE_URL=... bun run src/commands/auth.ts revoke "claude-desktop"
- *   DATABASE_URL=... bun run src/commands/auth.ts test <url> --token <token>
+ *
+ * Both paths require DATABASE_URL or GBRAIN_DATABASE_URL (except `test`,
+ * which only hits the remote URL and doesn't need a local DB).
  */
 import postgres from 'postgres';
 import { createHash, randomBytes } from 'crypto';
 
-const DATABASE_URL = process.env.DATABASE_URL || process.env.GBRAIN_DATABASE_URL;
-if (!DATABASE_URL && process.argv[2] !== 'test') {
-  console.error('Set DATABASE_URL or GBRAIN_DATABASE_URL environment variable.');
-  process.exit(1);
+function getDatabaseUrl(requireDb: boolean): string | undefined {
+  const url = process.env.DATABASE_URL || process.env.GBRAIN_DATABASE_URL;
+  if (!url && requireDb) {
+    console.error('Set DATABASE_URL or GBRAIN_DATABASE_URL environment variable.');
+    process.exit(1);
+  }
+  return url;
 }
 
 function hashToken(token: string): string {
@@ -27,7 +36,7 @@ function generateToken(): string {
 
 async function create(name: string) {
   if (!name) { console.error('Usage: auth create <name>'); process.exit(1); }
-  const sql = postgres(DATABASE_URL!);
+  const sql = postgres(getDatabaseUrl(true)!);
   const token = generateToken();
   const hash = hashToken(token);
 
@@ -53,7 +62,7 @@ async function create(name: string) {
 }
 
 async function list() {
-  const sql = postgres(DATABASE_URL!);
+  const sql = postgres(getDatabaseUrl(true)!);
   try {
     const rows = await sql`
       SELECT name, created_at, last_used_at, revoked_at
@@ -80,7 +89,7 @@ async function list() {
 
 async function revoke(name: string) {
   if (!name) { console.error('Usage: auth revoke <name>'); process.exit(1); }
-  const sql = postgres(DATABASE_URL!);
+  const sql = postgres(getDatabaseUrl(true)!);
   try {
     const result = await sql`
       UPDATE access_tokens SET revoked_at = now()
@@ -216,26 +225,38 @@ async function test(url: string, token: string) {
   console.log(`\n🧠 Your brain is live! (${elapsed}s)`);
 }
 
-// CLI dispatch
-const [cmd, ...args] = process.argv.slice(2);
-switch (cmd) {
-  case 'create': await create(args[0]); break;
-  case 'list': await list(); break;
-  case 'revoke': await revoke(args[0]); break;
-  case 'test': {
-    const tokenIdx = args.indexOf('--token');
-    const url = args.find(a => !a.startsWith('--') && a !== args[tokenIdx + 1]);
-    const token = tokenIdx >= 0 ? args[tokenIdx + 1] : '';
-    await test(url || '', token || '');
-    break;
-  }
-  default:
-    console.log(`GBrain Token Management
+/**
+ * Entry point for the `gbrain auth` CLI subcommand. Also reused by the
+ * direct-script path (see bottom of file) so `bun run src/commands/auth.ts`
+ * still works.
+ */
+export async function runAuth(args: string[]): Promise<void> {
+  const [cmd, ...rest] = args;
+  switch (cmd) {
+    case 'create': await create(rest[0]); return;
+    case 'list': await list(); return;
+    case 'revoke': await revoke(rest[0]); return;
+    case 'test': {
+      const tokenIdx = rest.indexOf('--token');
+      const url = rest.find(a => !a.startsWith('--') && a !== rest[tokenIdx + 1]);
+      const token = tokenIdx >= 0 ? rest[tokenIdx + 1] : '';
+      await test(url || '', token || '');
+      return;
+    }
+    default:
+      console.log(`GBrain Token Management
 
 Usage:
-  bun run src/commands/auth.ts create <name>      Create a new access token
-  bun run src/commands/auth.ts list               List all tokens
-  bun run src/commands/auth.ts revoke <name>       Revoke a token
-  bun run src/commands/auth.ts test <url> --token <token>  Smoke test a remote MCP server
+  gbrain auth create <name>           Create a new access token
+  gbrain auth list                    List all tokens
+  gbrain auth revoke <name>           Revoke a token
+  gbrain auth test <url> --token <t>  Smoke-test a remote MCP server
 `);
+  }
+}
+
+// Direct-script entry point — only runs when this file is invoked as the main module
+// (e.g. `bun run src/commands/auth.ts ...`). When imported by cli.ts, this block is skipped.
+if (import.meta.main) {
+  await runAuth(process.argv.slice(2));
 }

src/commands/doctor.ts

@@ -249,25 +249,29 @@ export async function runDoctor(engine: BrainEngine | null, args: string[], dbSo
   // Without this doctor check, users see "sync blocked" and have no
   // surface showing which files to fix.
   try {
-    const { unacknowledgedSyncFailures, loadSyncFailures } = await import('../core/sync.ts');
+    const { unacknowledgedSyncFailures, loadSyncFailures, summarizeFailuresByCode } = await import('../core/sync.ts');
     const unacked = unacknowledgedSyncFailures();
     const all = loadSyncFailures();
     if (unacked.length > 0) {
+      const codeSummary = summarizeFailuresByCode(unacked);
+      const codeBreakdown = codeSummary.map(s => `${s.code}=${s.count}`).join(', ');
       const preview = unacked.slice(0, 3).map(f => `${f.path} (${f.error.slice(0, 60)})`).join('; ');
       checks.push({
         name: 'sync_failures',
         status: 'warn',
         message:
-          `${unacked.length} unacknowledged sync failure(s). ${preview}` +
+          `${unacked.length} unacknowledged sync failure(s) [${codeBreakdown}]. ${preview}` +
           `${unacked.length > 3 ? `, and ${unacked.length - 3} more` : ''}. ` +
           `Fix the file(s) and re-run 'gbrain sync', or use 'gbrain sync --skip-failed' to acknowledge.`,
       });
     } else if (all.length > 0) {
-      // Acknowledged-only: informational, not a warning.
+      // Acknowledged-only: show code breakdown for visibility.
+      const ackedSummary = summarizeFailuresByCode(all);
+      const ackedBreakdown = ackedSummary.map(s => `${s.code}=${s.count}`).join(', ');
       checks.push({
         name: 'sync_failures',
         status: 'ok',
-        message: `${all.length} historical sync failure(s), all acknowledged.`,
+        message: `${all.length} historical sync failure(s), all acknowledged [${ackedBreakdown}].`,
       });
     }
   } catch {

src/commands/export.ts

@@ -1,16 +1,105 @@
-import { writeFileSync, mkdirSync } from 'fs';
+import { writeFileSync, mkdirSync, existsSync } from 'fs';
 import { join, dirname } from 'path';
 import type { BrainEngine } from '../core/engine.ts';
 import { serializeMarkdown } from '../core/markdown.ts';
 import { createProgress } from '../core/progress.ts';
 import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts';
+import { loadStorageConfig, isDbOnly } from '../core/storage-config.ts';
+import { getDefaultSourcePath } from '../core/source-resolver.ts';
+import type { PageType } from '../core/types.ts';
 
 export async function runExport(engine: BrainEngine, args: string[]) {
   const dirIdx = args.indexOf('--dir');
   const outDir = dirIdx !== -1 ? args[dirIdx + 1] : './export';
 
-  const pages = await engine.listPages({ limit: 100000 });
-  console.log(`Exporting ${pages.length} pages to ${outDir}/`);
+  const repoIdx = args.indexOf('--repo');
+  const explicitRepoPath = repoIdx !== -1 ? args[repoIdx + 1] : null;
+
+  const typeIdx = args.indexOf('--type');
+  const typeFilter = typeIdx !== -1 ? (args[typeIdx + 1] as PageType) : undefined;
+
+  const slugPrefixIdx = args.indexOf('--slug-prefix');
+  const slugPrefix = slugPrefixIdx !== -1 ? args[slugPrefixIdx + 1] : undefined;
+
+  const restoreOnly = args.includes('--restore-only');
+
+  // Resolution chain (D5): explicit --repo → typed sources.getDefault() →
+  // hard-error for restore-only paths (never fall through to cwd).
+  // For non-restore exports, repoPath stays null because regular export
+  // doesn't need a brain repo to run (D26 — exports include everything).
+  let repoPath: string | null = explicitRepoPath;
+  if (restoreOnly && !repoPath) {
+    repoPath = await getDefaultSourcePath(engine);
+    if (!repoPath) {
+      console.error(
+        `Error: gbrain export --restore-only requires --repo <path> or a configured\n` +
+          `default source with a local_path. Run \`gbrain sources list\` to inspect\n` +
+          `sources, or pass --repo explicitly.`,
+      );
+      process.exit(1);
+    }
+  }
+
+  // Load storage configuration if repo path is provided
+  const storageConfig = repoPath ? loadStorageConfig(repoPath) : null;
+
+  // D5 + Codex P0: refuse --restore-only when there's no storage config to
+  // scope the restore. Without storageConfig, the selective filter (db_only
+  // pages missing on disk) can't run, and falling through to the full
+  // listPages export silently dumps the entire DB. Catch this before any
+  // page query fires.
+  if (restoreOnly && !storageConfig) {
+    console.error(
+      `Error: gbrain export --restore-only requires a storage tiering config\n` +
+        `(gbrain.yml with a "storage:" section) at ${repoPath}/gbrain.yml.\n` +
+        `Without it, there's nothing to scope the restore to.\n` +
+        `Run \`gbrain storage status\` to inspect the current configuration.`,
+    );
+    process.exit(1);
+  }
+  
+  // Build filters. slugPrefix is engine-side (Issue #13) — no in-memory
+  // post-filter, no full-table load.
+  const filters: import('../core/types.ts').PageFilters = { limit: 100000 };
+  if (typeFilter) filters.type = typeFilter;
+  if (slugPrefix) filters.slugPrefix = slugPrefix;
+
+  let pages: import('../core/types.ts').Page[];
+
+  // Restore-only path: query each db_only directory with slugPrefix instead
+  // of loading every page in the brain. On a 200K-page brain where 95% is
+  // db_only, this is roughly the same load — but on brains where only 5K
+  // out of 200K are db_only, this is a ~40x reduction.
+  if (restoreOnly && repoPath && storageConfig) {
+    const seen = new Set<string>();
+    pages = [];
+    for (const dir of storageConfig.db_only) {
+      const tierFilters: import('../core/types.ts').PageFilters = {
+        ...filters,
+        slugPrefix: filters.slugPrefix
+          ? // If user passed --slug-prefix, only include tier dirs that start with it.
+            (dir.startsWith(filters.slugPrefix) ? dir : undefined)
+          : dir,
+      };
+      if (!tierFilters.slugPrefix) continue;
+      const tierPages = await engine.listPages(tierFilters);
+      for (const p of tierPages) {
+        if (seen.has(p.slug)) continue;
+        seen.add(p.slug);
+        if (!isDbOnly(p.slug, storageConfig)) continue; // belt-and-suspenders
+        const filePath = join(repoPath, p.slug + '.md');
+        if (existsSync(filePath)) continue;
+        pages.push(p);
+      }
+    }
+  } else {
+    pages = await engine.listPages(filters);
+  }
+  if (restoreOnly) {
+    console.log(`Restoring ${pages.length} db_only pages to ${outDir}/`);
+  } else {
+    console.log(`Exporting ${pages.length} pages to ${outDir}/`);
+  }
 
   // Progress on stderr so stdout stays clean for scripts parsing counts.
   const progress = createProgress(cliOptsToProgressOptions(getCliOptions()));
@@ -52,5 +141,9 @@ export async function runExport(engine: BrainEngine, args: string[]) {
 
   progress.finish();
   // Stdout summary preserved so scripts that grep for "Exported N pages" keep working.
-  console.log(`Exported ${exported} pages to ${outDir}/`);
+  if (restoreOnly) {
+    console.log(`Restored ${exported} pages to ${outDir}/`);
+  } else {
+    console.log(`Exported ${exported} pages to ${outDir}/`);
+  }
 }

src/commands/import.ts

@@ -34,7 +34,17 @@ export async function runImport(engine: BrainEngine, args: string[], opts: { com
   const jsonOutput = args.includes('--json');
   const workersIdx = args.indexOf('--workers');
   const workersArg = workersIdx !== -1 ? args[workersIdx + 1] : null;
-  const workerCount = workersArg ? parseInt(workersArg, 10) : 1;
+  // v0.22.13 (PR #490 Q2): shared parseWorkers helper rejects bad input
+  // (--workers 0, -3, "foo") with a loud error instead of silently falling
+  // through to 1. Mirrors sync.ts's flag handling.
+  const { parseWorkers } = await import('../core/sync-concurrency.ts');
+  let workerCount: number;
+  try {
+    workerCount = parseWorkers(workersArg ?? undefined) ?? 1;
+  } catch (e) {
+    console.error(e instanceof Error ? e.message : String(e));
+    process.exit(1);
+  }
   // Find dir: first non-flag arg that isn't a value for --workers
   const flagValues = new Set<number>();
   if (workersIdx !== -1) flagValues.add(workersIdx + 1);
@@ -141,40 +151,57 @@ export async function runImport(engine: BrainEngine, args: string[], opts: { com
   }
 
   if (actualWorkers > 1) {
-    // Parallel: create per-worker engine instances with small pool
-    // PGLite is single-connection, so parallel workers are only for Postgres
+    // v0.22.13 (PR #490 A1 + Q3): use engine.kind discriminator (not config.engine
+    // string sniff) and fall back to serial when database_url is unset. Both
+    // checks belt-and-suspenders so we never crash on a null assertion.
     const config = loadConfig();
-    if (config?.engine === 'pglite') {
-      // PGLite: sequential import through single engine
+    if (engine.kind === 'pglite' || !config?.database_url) {
       for (const file of files) {
         await processFile(engine, file);
       }
     } else {
-    const { PostgresEngine } = await import('../core/postgres-engine.ts');
-    const { resolvePoolSize } = await import('../core/db.ts');
-    // Default per-worker pool is 2 (small, parallel import case). Users on
-    // constrained poolers (e.g. Supabase port 6543) can cap below this via
-    // GBRAIN_POOL_SIZE=1.
-    const workerPoolSize = Math.min(2, resolvePoolSize(2));
-    const workerEngines = await Promise.all(
-      Array.from({ length: actualWorkers }, async () => {
-        const eng = new PostgresEngine();
-        await eng.connect({ database_url: config!.database_url!, poolSize: workerPoolSize });
-        return eng;
-      })
-    );
+      const { PostgresEngine } = await import('../core/postgres-engine.ts');
+      const { resolvePoolSize } = await import('../core/db.ts');
+      // Default per-worker pool is 2 (small, parallel import case). Users on
+      // constrained poolers (e.g. Supabase port 6543) can cap below this via
+      // GBRAIN_POOL_SIZE=1.
+      const workerPoolSize = Math.min(2, resolvePoolSize(2));
+      const databaseUrl = config.database_url;
 
-    // Thread-safe queue: use an atomic index counter instead of array.shift()
-    let queueIndex = 0;
-    await Promise.all(workerEngines.map(async (eng) => {
-      while (true) {
-        const idx = queueIndex++;
-        if (idx >= files.length) break;
-        await processFile(eng, files[idx]);
+      // v0.22.13 (PR #490 A2): connect workers serially so a partial failure
+      // leaves us with the connected ones already pushed onto workerEngines
+      // for the finally-block cleanup. The prior Promise.all could leak any
+      // engine that connected before another's connect() rejected.
+      const workerEngines: InstanceType<typeof PostgresEngine>[] = [];
+      try {
+        for (let i = 0; i < actualWorkers; i++) {
+          const eng = new PostgresEngine();
+          await eng.connect({ database_url: databaseUrl, poolSize: workerPoolSize });
+          workerEngines.push(eng);
+        }
+
+        // Thread-safe queue: atomic index counter (JS is single-threaded; the
+        // read-then-increment happens between awaits so no lock is needed).
+        let queueIndex = 0;
+        await Promise.all(workerEngines.map(async (eng) => {
+          while (true) {
+            const idx = queueIndex++;
+            if (idx >= files.length) break;
+            await processFile(eng, files[idx]);
+          }
+        }));
+      } finally {
+        // v0.22.13 (PR #490 A2): try/finally guarantees cleanup even when the
+        // worker loop throws. Each disconnect is best-effort — one failing
+        // disconnect must not strand the others.
+        await Promise.all(
+          workerEngines.map(e =>
+            e.disconnect().catch((err: unknown) =>
+              console.error(`  worker disconnect failed: ${err instanceof Error ? err.message : String(err)}`),
+            ),
+          ),
+        );
       }
-    }));
-
-    await Promise.all(workerEngines.map(e => e.disconnect()));
     } // end else (postgres parallel)
   } else {
     // Sequential: use the provided engine

src/commands/integrity.ts

@@ -31,6 +31,7 @@ import { join, dirname } from 'path';
 import { loadConfig, toEngineConfig } from '../core/config.ts';
 import { createEngine } from '../core/engine-factory.ts';
 import type { BrainEngine } from '../core/engine.ts';
+import * as db from '../core/db.ts';
 import { BrainWriter } from '../core/output/writer.ts';
 import {
   getDefaultRegistry,
@@ -266,6 +267,12 @@ export interface IntegrityScanOptions {
   limit?: number;
   /** Slug prefix filter (e.g. "people") — matches slugs starting with `${typeFilter}/`. */
   typeFilter?: string;
+  /**
+   * When true (default), batch-load pages via a single SQL query instead of
+   * sequential getPage() calls. Falls back to sequential on error (e.g. PGLite).
+   * Eliminates 500 round-trips through PgBouncer that caused doctor timeouts.
+   */
+  batchLoad?: boolean;
 }
 
 export interface IntegrityScanResult {
@@ -287,7 +294,29 @@ export async function scanIntegrity(
   engine: BrainEngine,
   opts: IntegrityScanOptions = {},
 ): Promise<IntegrityScanResult> {
-  const { limit = Infinity, typeFilter } = opts;
+  const { limit = Infinity, typeFilter, batchLoad = true } = opts;
+
+  // Fast path: single SQL query instead of N sequential getPage() calls.
+  // Eliminates ~500 round-trips through PgBouncer that caused doctor to
+  // timeout on transaction-mode pooling. Postgres-only: PGLite has no
+  // postgres.js connection, so the gate keeps the GBRAIN_DEBUG fallback
+  // log clean for real Postgres errors instead of expected PGLite skips.
+  if (batchLoad && limit !== Infinity && engine.kind === 'postgres') {
+    try {
+      return await scanIntegrityBatch(limit, typeFilter);
+    } catch (err) {
+      // GBRAIN_DEBUG=1 surfaces real Postgres errors (deadlock, connection
+      // drop, SQL bug) that would otherwise vanish into the sequential
+      // fallback. Quiet by default since the fallback is harmless.
+      if (process.env.GBRAIN_DEBUG) {
+        console.error(
+          '[integrity] batch path failed, falling back to sequential:',
+          err instanceof Error ? err.message : err,
+        );
+      }
+    }
+  }
+
   const allSlugs = [...(await engine.getAllSlugs())].sort();
 
   const bareHits: BareTweetHit[] = [];
@@ -316,6 +345,52 @@ export async function scanIntegrity(
   return { pagesScanned, bareHits, externalHits, topPages };
 }
 
+/**
+ * Batch-load integrity scan: fetches all candidate pages in a single SQL
+ * query, then scans in-memory. Reduces PgBouncer round-trips from ~500 to 1.
+ */
+async function scanIntegrityBatch(
+  limit: number,
+  typeFilter?: string,
+): Promise<IntegrityScanResult> {
+  const sql = db.getConnection();
+  const typeCondition = typeFilter ? sql`AND slug LIKE ${typeFilter + '/%'}` : sql``;
+  // Boolean validate is the documented contract; stringly-typed 'false' (quoted
+  // YAML) diverges from the sequential path's strict === false check. Intentional
+  // — gbrain lint should reject stringly-typed validate at write time.
+  const validateCondition = sql`AND (frontmatter->>'validate' IS NULL OR frontmatter->>'validate' != 'false')`;
+
+  // DISTINCT ON (slug) mirrors getAllSlugs()'s Set<string> semantics: multi-source
+  // brains can have the same slug under multiple source_ids (UNIQUE(source_id, slug)
+  // since v0.18.0); we want one scan per slug, not one per row.
+  const rows = await sql`
+    SELECT DISTINCT ON (slug) slug, compiled_truth, frontmatter
+    FROM pages
+    WHERE 1=1 ${typeCondition} ${validateCondition}
+    ORDER BY slug
+    LIMIT ${limit}
+  `;
+
+  const bareHits: BareTweetHit[] = [];
+  const externalHits: ExternalLinkHit[] = [];
+
+  for (const row of rows) {
+    const slug = row.slug as string;
+    const compiledTruth = row.compiled_truth as string;
+    bareHits.push(...findBareTweetHits(compiledTruth, slug));
+    externalHits.push(...findExternalLinks(compiledTruth, slug));
+  }
+
+  const byPage = new Map<string, number>();
+  for (const h of bareHits) byPage.set(h.slug, (byPage.get(h.slug) ?? 0) + 1);
+  const topPages = [...byPage.entries()]
+    .sort((a, b) => b[1] - a[1])
+    .slice(0, 10)
+    .map(([slug, count]) => ({ slug, count }));
+
+  return { pagesScanned: rows.length, bareHits, externalHits, topPages };
+}
+
 // ---------------------------------------------------------------------------
 // auto — three-bucket repair
 // ---------------------------------------------------------------------------

src/commands/jobs.ts

@@ -864,8 +864,40 @@ export async function registerBuiltinHandlers(worker: MinionWorker, engine: Brai
     const { performSync } = await import('./sync.ts');
     const repoPath = typeof job.data.repoPath === 'string' ? job.data.repoPath : undefined;
     const noPull = !!job.data.noPull;
+    // noEmbed defaults to true (embed is a separate job — submit `embed --stale`
+    // after sync, OR run via the autopilot cycle which has its own embed phase).
+    // Caller can opt in by passing { noEmbed: false } in job params.
     const noEmbed = job.data.noEmbed !== false;
-    const result = await performSync(engine, { repoPath, noPull, noEmbed });
+    // v0.22.13 (PR #490 CODEX-1): resolve sourceId from job param OR by looking
+    // up the sources row for repoPath. Mirrors cycle.ts:480 — without this, a
+    // multi-source brain reads the global config.sync.last_commit anchor
+    // instead of sources.last_commit, which on a regularly-GC'd repo can drop
+    // out of git history and trigger 30-min full reimports every cycle.
+    let sourceId: string | undefined =
+      typeof job.data.sourceId === 'string' ? job.data.sourceId : undefined;
+    if (!sourceId && repoPath) {
+      try {
+        const rows = await engine.executeRaw<{ id: string }>(
+          `SELECT id FROM sources WHERE local_path = $1 LIMIT 1`,
+          [repoPath],
+        );
+        sourceId = rows[0]?.id;
+      } catch {
+        // sources table may not exist on very old brains — fall through to
+        // global config.sync.* anchor in performSync.
+      }
+    }
+    // v0.22.13 (PR #490 CODEX-4): route concurrency through the shared
+    // autoConcurrency helper instead of hardcoded 4. PGLite engines stay
+    // serial (forced 1); explicit job param wins; auto path defaults are
+    // applied inside performSync against the resolved file count.
+    const concurrencyOverride = typeof job.data.concurrency === 'number'
+      ? job.data.concurrency
+      : undefined;
+    const result = await performSync(engine, {
+      repoPath, sourceId, noPull, noEmbed,
+      concurrency: concurrencyOverride,
+    });
     return result;
   });
 
@@ -948,10 +980,19 @@ export async function registerBuiltinHandlers(worker: MinionWorker, engine: Brai
       ? job.data.repoPath
       : (await engine.getConfig('sync.repo_path')) ?? '.';
 
+    // Allow callers to select phases via job data (e.g. skip embed for
+    // fast cycles). Validates against ALL_PHASES to prevent injection.
+    const { ALL_PHASES } = await import('../core/cycle.ts');
+    const validPhases = new Set(ALL_PHASES);
+    const requestedPhases = Array.isArray(job.data.phases)
+      ? (job.data.phases as string[]).filter(p => validPhases.has(p as any))
+      : undefined;
+
     const report = await runCycle(engine, {
       brainDir: repoPath,
       pull: true, // autopilot daemon opts into git pull
       signal: job.signal, // propagate abort so cycle bails on timeout/cancel
+      ...(requestedPhases && requestedPhases.length > 0 ? { phases: requestedPhases as any } : {}),
       yieldBetweenPhases: async () => {
         // Yield to the event loop so worker lock-renewal can fire.
         await new Promise<void>(r => setImmediate(r));

src/commands/serve.ts

@@ -1,7 +1,19 @@
 import type { BrainEngine } from '../core/engine.ts';
 import { startMcpServer } from '../mcp/server.ts';
+import { startHttpTransport } from '../mcp/http-transport.ts';
 
-export async function runServe(engine: BrainEngine) {
-  console.error('Starting GBrain MCP server (stdio)...');
-  await startMcpServer(engine);
+export async function runServe(engine: BrainEngine, args: string[] = []) {
+  const useHttp = args.includes('--http');
+  const portIdx = args.indexOf('--port');
+  const port = portIdx >= 0 ? parseInt(args[portIdx + 1]) || 8787 : 8787;
+
+  if (useHttp) {
+    console.error(`Starting GBrain MCP server (HTTP on port ${port})...`);
+    await startHttpTransport({ port, engine });
+    // Keep alive
+    await new Promise(() => {});
+  } else {
+    console.error('Starting GBrain MCP server (stdio)...');
+    await startMcpServer(engine);
+  }
 }

src/commands/storage.ts

@@ -0,0 +1,245 @@
+import { join } from 'path';
+import type { BrainEngine } from '../core/engine.ts';
+import { loadStorageConfig, validateStorageConfig, getStorageTier } from '../core/storage-config.ts';
+import type { StorageConfig, StorageTier } from '../core/storage-config.ts';
+import { walkBrainRepo, type DiskFileEntry } from '../core/disk-walk.ts';
+import { getDefaultSourcePath } from '../core/source-resolver.ts';
+
+/**
+ * Distinct nominal types for the two tier-keyed numeric maps. Both shapes
+ * are `Record<StorageTier, number>` structurally — but they carry
+ * semantically different units (page COUNT vs disk BYTES). Distinct types
+ * make accidental swaps a compile-time error rather than a silent display
+ * bug. Issue #11 of the eng review.
+ */
+export type PageCountsByTier = Record<StorageTier, number> & { __brand?: 'page-counts' };
+export type DiskUsageByTier = Record<StorageTier, number> & { __brand?: 'disk-bytes' };
+
+/**
+ * Pure-data result of a storage-status query. No side effects, no I/O
+ * beyond the engine call and one filesystem walk. Consumed by both the
+ * JSON formatter and the human formatter; kept narrow so it's a stable
+ * MCP/scripting contract (D14: storage_status is read-only MCP-exposed).
+ */
+export interface StorageStatusResult {
+  config: StorageConfig | null;
+  repoPath: string | null;
+  totalPages: number;
+  pagesByTier: PageCountsByTier;
+  missingFiles: Array<{ slug: string; expectedPath: string }>;
+  diskUsageByTier: DiskUsageByTier;
+  warnings: string[];
+}
+
+// ── Dispatcher ────────────────────────────────────────────
+
+export async function runStorage(engine: BrainEngine, args: string[]): Promise<void> {
+  const subcommand = args[0];
+  if (!subcommand || subcommand === 'status') {
+    await runStorageStatus(engine, args.slice(1));
+    return;
+  }
+  console.error(`Unknown storage subcommand: ${subcommand}`);
+  console.error('Available subcommands: status');
+  process.exit(1);
+}
+
+async function runStorageStatus(engine: BrainEngine, args: string[]): Promise<void> {
+  warnIfPGLite(engine);
+
+  // Resolution chain (D5, Issue #3): explicit --repo → typed accessor → null.
+  // No cwd fallback. The original silent footgun is dead.
+  let repoPath: string | null = null;
+  const repoIdx = args.indexOf('--repo');
+  if (repoIdx !== -1 && args[repoIdx + 1]) {
+    repoPath = args[repoIdx + 1];
+  } else {
+    repoPath = await getDefaultSourcePath(engine);
+  }
+
+  const result = await getStorageStatus(engine, repoPath);
+
+  if (args.includes('--json')) {
+    console.log(formatStorageStatusJson(result));
+    return;
+  }
+  console.log(formatStorageStatusHuman(result));
+}
+
+/**
+ * D4: storage tiering on PGLite is a partial feature. The "DB" the pages
+ * live in IS the local file gbrain uses for everything else, so "db_only"
+ * has no real offload effect. The .gitignore management still helps
+ * (keeps bulk content out of git history), so we warn but proceed.
+ *
+ * Once-per-process via a module-local flag — sub-commands invoked from a
+ * single CLI run share the same warning.
+ */
+let _pgliteWarned = false;
+function warnIfPGLite(engine: BrainEngine): void {
+  if (_pgliteWarned) return;
+  if (engine.kind !== 'pglite') return;
+  _pgliteWarned = true;
+  console.warn(
+    `Note: storage tiering has limited effect on PGLite — pages live in your ` +
+      `local database file regardless of tier. The .gitignore management still ` +
+      `keeps bulk content out of git history. To get full tiering, migrate to ` +
+      `Postgres with \`gbrain migrate --to supabase\`.`,
+  );
+}
+
+/** Reset for tests. */
+export function __resetPGLiteWarn(): void {
+  _pgliteWarned = false;
+}
+
+// ── Pure data ─────────────────────────────────────────────
+
+/**
+ * Compute the storage status against the given engine + brain repo path.
+ *
+ * Side-effect-free apart from the engine.listPages call and one recursive
+ * filesystem walk. Pure for testability — formatters are tested separately.
+ *
+ * Returns null `config` when no gbrain.yml is present at repoPath. In that
+ * case pagesByTier is all zeros for db_tracked/db_only and totals roll up
+ * into unspecified.
+ */
+export async function getStorageStatus(
+  engine: BrainEngine,
+  repoPath: string | null,
+): Promise<StorageStatusResult> {
+  const config = repoPath ? loadStorageConfig(repoPath) : null;
+  const warnings = config ? validateStorageConfig(config) : [];
+
+  const pagesByTier: PageCountsByTier = { db_tracked: 0, db_only: 0, unspecified: 0 };
+  const diskUsageByTier: DiskUsageByTier = { db_tracked: 0, db_only: 0, unspecified: 0 };
+  const missingFiles: Array<{ slug: string; expectedPath: string }> = [];
+
+  // Single recursive walk of the brain repo (Issue #14). Replaces per-page
+  // existsSync+statSync — was ~400K syscalls on 200K-page brains, now ~one
+  // per directory + one stat per .md file, plus O(1) lookups below.
+  const fileMap: Map<string, DiskFileEntry> = repoPath ? walkBrainRepo(repoPath) : new Map();
+
+  const pages = await engine.listPages({ limit: 1_000_000 });
+
+  for (const page of pages) {
+    const tier = config ? getStorageTier(page.slug, config) : 'unspecified';
+    pagesByTier[tier]++;
+    if (!repoPath) continue;
+    const entry = fileMap.get(page.slug);
+    if (entry) {
+      diskUsageByTier[tier] += entry.size;
+    } else if (config && tier === 'db_only') {
+      missingFiles.push({ slug: page.slug, expectedPath: join(repoPath, page.slug + '.md') });
+    }
+  }
+
+  return {
+    config,
+    repoPath,
+    totalPages: pages.length,
+    pagesByTier,
+    missingFiles,
+    diskUsageByTier,
+    warnings,
+  };
+}
+
+// ── JSON formatter ────────────────────────────────────────
+
+/**
+ * Serialize StorageStatusResult to a stable JSON contract. Indented for
+ * human readability; agents/orchestrators can parse with a standard
+ * JSON.parse. Schema is the StorageStatusResult interface above.
+ */
+export function formatStorageStatusJson(result: StorageStatusResult): string {
+  return JSON.stringify(result, null, 2);
+}
+
+// ── Human formatter ───────────────────────────────────────
+
+/**
+ * Render StorageStatusResult to ASCII text suitable for terminal output.
+ * D10 lock: ASCII separators only — universally portable. No unicode
+ * box-drawing.
+ */
+export function formatStorageStatusHuman(result: StorageStatusResult): string {
+  const lines: string[] = [];
+  lines.push('Storage Status');
+  lines.push('==============');
+  lines.push('');
+
+  if (!result.config) {
+    lines.push('No gbrain.yml configuration found.');
+    if (result.repoPath) lines.push(`Checked: ${result.repoPath}/gbrain.yml`);
+    lines.push('');
+    lines.push('All pages are stored in git by default.');
+    lines.push(`Total pages: ${result.totalPages}`);
+    return lines.join('\n');
+  }
+
+  lines.push(`Repository: ${result.repoPath}`);
+  lines.push(`Total pages: ${result.totalPages}`);
+  lines.push('');
+  lines.push('Storage Tiers:');
+  lines.push('-------------');
+  lines.push(`DB tracked:     ${result.pagesByTier.db_tracked.toLocaleString()} pages`);
+  lines.push(`DB only:        ${result.pagesByTier.db_only.toLocaleString()} pages`);
+  lines.push(`Unspecified:    ${result.pagesByTier.unspecified.toLocaleString()} pages`);
+
+  if (result.diskUsageByTier.db_tracked > 0 || result.diskUsageByTier.db_only > 0) {
+    lines.push('');
+    lines.push('Disk Usage:');
+    lines.push('-----------');
+    if (result.diskUsageByTier.db_tracked > 0) {
+      lines.push(`DB tracked:     ${formatBytes(result.diskUsageByTier.db_tracked)}`);
+    }
+    if (result.diskUsageByTier.db_only > 0) {
+      lines.push(`DB only:        ${formatBytes(result.diskUsageByTier.db_only)}`);
+    }
+    if (result.diskUsageByTier.unspecified > 0) {
+      lines.push(`Unspecified:    ${formatBytes(result.diskUsageByTier.unspecified)}`);
+    }
+  }
+
+  if (result.missingFiles.length > 0) {
+    lines.push('');
+    lines.push('Missing Files (need restore):');
+    lines.push('-----------------------------');
+    for (const missing of result.missingFiles.slice(0, 10)) {
+      lines.push(`  ${missing.slug}`);
+    }
+    if (result.missingFiles.length > 10) {
+      lines.push(`  ... and ${result.missingFiles.length - 10} more`);
+    }
+    lines.push('');
+    lines.push(`Use: gbrain export --restore-only --repo "${result.repoPath}"`);
+  }
+
+  if (result.warnings.length > 0) {
+    lines.push('');
+    lines.push('Warnings:');
+    lines.push('---------');
+    for (const warning of result.warnings) lines.push(`  ! ${warning}`);
+  }
+
+  lines.push('');
+  lines.push('Configuration:');
+  lines.push('--------------');
+  lines.push('DB tracked directories:');
+  for (const dir of result.config.db_tracked) lines.push(`  - ${dir}`);
+  lines.push('');
+  lines.push('DB-only directories:');
+  for (const dir of result.config.db_only) lines.push(`  - ${dir}`);
+
+  return lines.join('\n');
+}
+
+function formatBytes(bytes: number): string {
+  if (bytes === 0) return '0 B';
+  const k = 1024;
+  const sizes = ['B', 'KB', 'MB', 'GB', 'TB'];
+  const i = Math.floor(Math.log(bytes) / Math.log(k));
+  return parseFloat((bytes / Math.pow(k, i)).toFixed(1)) + ' ' + sizes[i];
+}

src/commands/sync.ts

@@ -1,9 +1,8 @@
-import { existsSync } from 'fs';
+import { existsSync, readFileSync, writeFileSync, statSync, readdirSync } from 'fs';
 import { execFileSync } from 'child_process';
 import { join, relative } from 'path';
 import type { BrainEngine } from '../core/engine.ts';
 import { importFile } from '../core/import-file.ts';
-import { readFileSync, statSync, readdirSync } from 'fs';
 import { createInterface } from 'readline';
 import {
   buildSyncManifest,
@@ -12,6 +11,7 @@ import {
   recordSyncFailures,
   unacknowledgedSyncFailures,
   acknowledgeSyncFailures,
+  formatCodeBreakdown,
 } from '../core/sync.ts';
 import { estimateTokens, CHUNKER_VERSION } from '../core/chunkers/code.ts';
 import { EMBEDDING_MODEL, estimateEmbeddingCostUsd } from '../core/embedding.ts';
@@ -19,6 +19,15 @@ import { errorFor, serializeError } from '../core/errors.ts';
 import type { SyncManifest } from '../core/sync.ts';
 import { createProgress } from '../core/progress.ts';
 import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts';
+import { loadConfig } from '../core/config.ts';
+import {
+  autoConcurrency,
+  shouldRunParallel,
+  parseWorkers,
+} from '../core/sync-concurrency.ts';
+import { tryAcquireDbLock, SYNC_LOCK_ID } from '../core/db-lock.ts';
+import { loadStorageConfig } from '../core/storage-config.ts';
+import { getDefaultSourcePath } from '../core/source-resolver.ts';
 
 export interface SyncResult {
   status: 'up_to_date' | 'synced' | 'first_sync' | 'dry_run' | 'blocked_by_failures';
@@ -157,6 +166,27 @@ export interface SyncOpts {
   sourceId?: string;
   /** Multi-repo: sync strategy override (markdown, code, auto). */
   strategy?: 'markdown' | 'code' | 'auto';
+  /**
+   * Number of parallel workers for the import phase. When > 1, each worker
+   * gets its own small Postgres connection pool and files are dispatched via
+   * an atomic queue index (same pattern as `import --workers N`).
+   *
+   * Deletes and renames remain serial (order-dependent).
+   * Default: undefined → auto-concurrency picks (`src/core/sync-concurrency.ts`).
+   *
+   * v0.22.13 (PR #490 Q1): when this is explicitly set, the >50-file floor
+   * is bypassed — explicit user intent beats the auto-path safety net.
+   */
+  concurrency?: number;
+  /**
+   * Internal: skip acquiring the gbrain-sync DB lock. Set by the cycle
+   * handler (cycle.ts) which already holds gbrain-cycle and therefore
+   * already serializes against other cycle runs. CLI sync, jobs handler,
+   * and any external caller leave this undefined so they take the lock.
+   *
+   * v0.22.13 (PR #490 CODEX-2). Not part of the public CLI surface.
+   */
+  skipLock?: boolean;
 }
 
 function git(repoPath: string, ...args: string[]): string {
@@ -250,6 +280,39 @@ async function writeChunkerVersion(
 }
 
 export async function performSync(engine: BrainEngine, opts: SyncOpts): Promise<SyncResult> {
+  // CODEX-2 (v0.22.13): cross-process writer lock for performSync. Two
+  // concurrent syncs can otherwise read the same last_commit anchor, both
+  // write last_commit unconditionally, and the last writer wins — including
+  // regressing the bookmark backwards. cycle.ts already takes gbrain-cycle
+  // for its broader scope; performSync (called from cycle, jobs handler,
+  // and CLI) takes gbrain-sync just for the writer window. The two ids
+  // nest cleanly: cycle holds gbrain-cycle, calls performSync, performSync
+  // takes gbrain-sync. Other callers serialize on gbrain-sync against
+  // each other AND against the cycle's sync phase.
+  //
+  // skipLock is reserved for callers that already serialize via another
+  // mechanism (none in v0.22.13; reserved for future).
+  let lockHandle: { release: () => Promise<void> } | null = null;
+  if (!opts.skipLock) {
+    lockHandle = await tryAcquireDbLock(engine, SYNC_LOCK_ID);
+    if (!lockHandle) {
+      throw new Error(
+        `Another sync is in progress (lock ${SYNC_LOCK_ID} held). ` +
+        `Wait for it to finish, or run 'gbrain doctor' if it has been more than 30 minutes.`,
+      );
+    }
+  }
+
+  try {
+    return await performSyncInner(engine, opts);
+  } finally {
+    if (lockHandle) {
+      try { await lockHandle.release(); } catch { /* best-effort release */ }
+    }
+  }
+}
+
+async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<SyncResult> {
   // Resolve repo path
   const repoPath = opts.repoPath || await readSyncAnchor(engine, opts.sourceId, 'repo_path');
   if (!repoPath) {
@@ -486,21 +549,41 @@ export async function performSync(engine: BrainEngine, opts: SyncOpts): Promise<
   // gate `sync.last_commit` advancement and record recoverable errors.
   const failedFiles: Array<{ path: string; error: string; line?: number }> = [];
   const addsAndMods = [...filtered.added, ...filtered.modified];
+
+  // v0.22.13 (PR #490 Q5): one source of truth for the concurrency decision.
+  // engine.kind === 'pglite' → forced 1; explicit opts.concurrency wins;
+  // auto path returns DEFAULT_PARALLEL_WORKERS only when fileCount > 100.
+  const explicitConcurrency = opts.concurrency !== undefined;
+  const effectiveConcurrency = autoConcurrency(engine, addsAndMods.length, opts.concurrency);
+  const runParallel = shouldRunParallel(effectiveConcurrency, addsAndMods.length, explicitConcurrency);
+
   if (addsAndMods.length > 0) {
     progress.start('sync.imports', addsAndMods.length);
-    for (const path of addsAndMods) {
-      const filePath = join(repoPath, path);
+
+    // Core import logic shared by serial and parallel paths.
+    // repoPath is validated non-null at the top of performSyncInner; narrow for TS.
+    const syncRepoPath = repoPath!;
+    async function importOnePath(eng: BrainEngine, path: string): Promise<void> {
+      const filePath = join(syncRepoPath, path);
       if (!existsSync(filePath)) {
+        // CODEX-3 (v0.22.13): a file the diff said exists at headCommit but
+        // is gone from disk means the working tree has drifted (someone ran
+        // `git checkout` / `git reset` mid-sync, or the file was deleted
+        // post-diff). Record as a failure so last_commit does NOT advance —
+        // the silent-skip-then-advance pathology was the bug.
+        failedFiles.push({
+          path,
+          error: 'file vanished mid-sync (working tree drifted from headCommit)',
+        });
         progress.tick(1, `skip:${path}`);
-        continue;
+        return;
       }
       try {
-        const result = await importFile(engine, filePath, path, { noEmbed });
+        const result = await importFile(eng, filePath, path, { noEmbed });
         if (result.status === 'imported') {
           chunksCreated += result.chunks;
           pagesAffected.push(result.slug);
         } else if (result.status === 'skipped' && (result as any).error) {
-          // importFile returned a non-throw skip with a reason.
           failedFiles.push({ path, error: String((result as any).error) });
         }
       } catch (e: unknown) {
@@ -510,9 +593,98 @@ export async function performSync(engine: BrainEngine, opts: SyncOpts): Promise<
       }
       progress.tick(1, path);
     }
+
+    if (runParallel) {
+      // A1 (v0.22.13): use engine.kind discriminator instead of config?.engine
+      // string compare or constructor.name sniff. Q3: belt-and-suspenders fall
+      // back to serial when database_url is unset, so we never crash on a null
+      // assertion if config is missing.
+      const config = loadConfig();
+      if (engine.kind === 'pglite' || !config?.database_url) {
+        for (const path of addsAndMods) {
+          await importOnePath(engine, path);
+        }
+      } else {
+        const { PostgresEngine } = await import('../core/postgres-engine.ts');
+        const { resolvePoolSize } = await import('../core/db.ts');
+        const workerPoolSize = Math.min(2, resolvePoolSize(2));
+        const workerCount = Math.min(effectiveConcurrency, addsAndMods.length);
+        const databaseUrl = config.database_url;
+
+        // Q4 (v0.22.13): banner on stderr so stdout stays clean for --json.
+        console.error(`  Parallel sync: ${workerCount} workers for ${addsAndMods.length} files`);
+
+        const workerEngines: InstanceType<typeof PostgresEngine>[] = [];
+        try {
+          // Connect workers one-by-one rather than Promise.all so a partial
+          // failure leaves us with the connected ones in workerEngines for
+          // the finally-block cleanup. The original code lost track of
+          // already-connected engines on any one failure.
+          for (let i = 0; i < workerCount; i++) {
+            const eng = new PostgresEngine();
+            await eng.connect({ database_url: databaseUrl, poolSize: workerPoolSize });
+            workerEngines.push(eng);
+          }
+
+          // Atomic queue index — JS is single-threaded; the read-then-increment
+          // happens between awaits, so no lock is needed.
+          let queueIndex = 0;
+          await Promise.all(
+            workerEngines.map(async (eng) => {
+              while (true) {
+                const idx = queueIndex++;
+                if (idx >= addsAndMods.length) break;
+                await importOnePath(eng, addsAndMods[idx]);
+              }
+            }),
+          );
+        } finally {
+          // A2 (v0.22.13): try/finally guarantees connection cleanup even when
+          // the worker loop throws (partial connect failure, OOM, mid-import
+          // signal). Each disconnect is best-effort — one worker failing to
+          // disconnect must not strand the others.
+          await Promise.all(
+            workerEngines.map((e) =>
+              e.disconnect().catch((err: unknown) =>
+                console.error(`  worker disconnect failed: ${err instanceof Error ? err.message : String(err)}`),
+              ),
+            ),
+          );
+        }
+      }
+    } else {
+      // Serial path (small auto diffs or explicit --workers 1).
+      for (const path of addsAndMods) {
+        await importOnePath(engine, path);
+      }
+    }
+
     progress.finish();
   }
 
+  // CODEX-3 (v0.22.13): head-drift gate. If git HEAD moved during the import
+  // window (someone ran `git checkout` or `git pull` in another terminal /
+  // sibling Conductor workspace), the chunks we just imported reflect a
+  // different tree than `headCommit` claims. Refuse to advance last_commit
+  // so the next sync re-walks against the new HEAD. The lock from CODEX-2
+  // prevents *this* gbrain process from stepping on itself; this gate
+  // catches drift caused by external `git` commands the lock cannot see.
+  try {
+    const currentHead = git(repoPath, 'rev-parse', 'HEAD');
+    if (currentHead !== headCommit) {
+      failedFiles.push({
+        path: '<head>',
+        error: `git HEAD drifted during sync: captured ${headCommit.slice(0, 8)}, now ${currentHead.slice(0, 8)}`,
+      });
+    }
+  } catch (e) {
+    // rev-parse failure is itself a drift signal (worktree disappeared).
+    failedFiles.push({
+      path: '<head>',
+      error: `git HEAD verification failed: ${e instanceof Error ? e.message : String(e)}`,
+    });
+  }
+
   const elapsed = Date.now() - start;
 
   // Bug 9 — gate the sync bookmark on success. If any per-file parse
@@ -522,9 +694,13 @@ export async function performSync(engine: BrainEngine, opts: SyncOpts): Promise<
   // current set, --retry-failed re-parses before running the normal sync.
   if (failedFiles.length > 0) {
     recordSyncFailures(failedFiles, headCommit);
+    // Emit structured summary grouped by error code so the operator
+    // can see *why* files failed, not just how many.
+    const codeBreakdown = formatCodeBreakdown(failedFiles);
     if (!opts.skipFailed) {
       console.error(
-        `\nSync blocked: ${failedFiles.length} file(s) failed to parse. ` +
+        `\nSync blocked: ${failedFiles.length} file(s) failed to parse:\n` +
+        `${codeBreakdown}\n\n` +
         `Fix the YAML frontmatter in the files above and re-run, or use ` +
         `'gbrain sync --skip-failed' to acknowledge and move on.`,
       );
@@ -547,8 +723,11 @@ export async function performSync(engine: BrainEngine, opts: SyncOpts): Promise<
     }
     // --skip-failed: acknowledge the now-recorded set and proceed.
     const acked = acknowledgeSyncFailures();
-    if (acked > 0) {
-      console.error(`  Acknowledged ${acked} failure(s) and advancing past them.`);
+    if (acked.count > 0) {
+      console.error(
+        `  Acknowledged ${acked.count} failure(s) and advancing past them:\n` +
+        `${formatCodeBreakdown(acked.summary)}`,
+      );
     }
   }
 
@@ -644,10 +823,18 @@ async function performFullSync(
     };
   }
 
-  console.log(`Running full import of ${repoPath}...`);
+  // v0.22.13 (PR #490 A1 + Q5): full sync is always "large" by definition
+  // (entire working tree). Auto-concurrency fires unconditionally for Postgres;
+  // PGLite stays serial because its engine is single-connection. Routes the
+  // policy through autoConcurrency() so it stays consistent with incremental
+  // sync and the jobs handler.
+  const FULL_SYNC_LARGE_MARKER = Number.MAX_SAFE_INTEGER;
+  const fullConcurrency = autoConcurrency(engine, FULL_SYNC_LARGE_MARKER, opts.concurrency);
+  console.log(`Running full import of ${repoPath}${fullConcurrency > 1 ? ` (${fullConcurrency} workers)` : ''}...`);
   const { runImport } = await import('./import.ts');
   const importArgs = [repoPath];
   if (opts.noEmbed) importArgs.push('--no-embed');
+  if (fullConcurrency > 1) importArgs.push('--workers', String(fullConcurrency));
   const result = await runImport(engine, importArgs, { commit: headCommit });
 
   // Bug 9 — gate the full-sync bookmark on success. runImport already
@@ -656,9 +843,11 @@ async function performFullSync(
   // the sync module owns the last_commit write. Respect the same gate.
   if (result.failures.length > 0) {
     recordSyncFailures(result.failures, headCommit);
+    const codeBreakdown = formatCodeBreakdown(result.failures);
     if (!opts.skipFailed) {
       console.error(
-        `\nFull sync blocked: ${result.failures.length} file(s) failed. ` +
+        `\nFull sync blocked: ${result.failures.length} file(s) failed:\n` +
+        `${codeBreakdown}\n\n` +
         `Fix the YAML in those files and re-run, or use '--skip-failed'.`,
       );
       await engine.setConfig('sync.last_run', new Date().toISOString());
@@ -675,7 +864,12 @@ async function performFullSync(
       };
     }
     const acked = acknowledgeSyncFailures();
-    if (acked > 0) console.error(`  Acknowledged ${acked} failure(s) and advancing past them.`);
+    if (acked.count > 0) {
+      console.error(
+        `  Acknowledged ${acked.count} failure(s) and advancing past them:\n` +
+        `${formatCodeBreakdown(acked.summary)}`,
+      );
+    }
   }
 
   // Persist sync state so next sync is incremental (C1 fix: was missing).
@@ -728,6 +922,17 @@ export async function runSync(engine: BrainEngine, args: string[]) {
   const jsonOut = args.includes('--json');
   const yesFlag = args.includes('--yes');
   const strategyArg = args.find((a, i) => args[i - 1] === '--strategy') as SyncOpts['strategy'] | undefined;
+  const concurrencyStr = args.find((a, i) => args[i - 1] === '--concurrency' || args[i - 1] === '--workers');
+  // v0.22.13 (PR #490 Q2): parseWorkers throws on '0', '-3', 'foo', '1.5' instead
+  // of silently falling through to auto-concurrency or NaN. Loud failure beats
+  // a 4-worker spawn from a typo.
+  let concurrency: number | undefined;
+  try {
+    concurrency = parseWorkers(concurrencyStr);
+  } catch (e) {
+    console.error(e instanceof Error ? e.message : String(e));
+    process.exit(1);
+  }
 
   // v0.18.0 Step 5: --source resolves to a sources(id) row. Falls back
   // to pre-v0.17 global config (sync.repo_path + sync.last_commit) when
@@ -820,10 +1025,18 @@ export async function runSync(engine: BrainEngine, args: string[]) {
         dryRun, full, noPull, noEmbed, skipFailed, retryFailed,
         sourceId: src.id,
         strategy: cfg.strategy,
+        concurrency,
       };
       try {
         const result = await performSync(engine, repoOpts);
         printSyncResult(result);
+        // Codex P2: --all loop must also manage .gitignore per-source. Without
+        // this, multi-source users who rely on `gbrain sync --all` never get
+        // the advertised db_only ignore rules unless they sync each repo
+        // individually.
+        if (result.status !== 'dry_run' && result.status !== 'blocked_by_failures') {
+          manageGitignore(src.local_path!, engine.kind);
+        }
       } catch (e: unknown) {
         console.error(`Error syncing ${src.name}: ${e instanceof Error ? e.message : String(e)}`);
       }
@@ -831,7 +1044,7 @@ export async function runSync(engine: BrainEngine, args: string[]) {
     return;
   }
 
-  const opts: SyncOpts = { repoPath, dryRun, full, noPull, noEmbed, skipFailed, retryFailed, sourceId, strategy: strategyArg };
+  const opts: SyncOpts = { repoPath, dryRun, full, noPull, noEmbed, skipFailed, retryFailed, sourceId, strategy: strategyArg, concurrency };
 
   // Bug 9 — --retry-failed: before running normal sync, clear acknowledgment
   // flags so the sync picks them up as fresh work. The actual re-attempt
@@ -850,6 +1063,18 @@ export async function runSync(engine: BrainEngine, args: string[]) {
   if (!watch) {
     const result = await performSync(engine, opts);
     printSyncResult(result);
+    // Issue #2 + eng-review pass-2 finding #1 + Codex P1: manage .gitignore ONLY
+    // on successful sync. Skip on dry-run (don't mutate disk in preview mode)
+    // and blocked_by_failures (sync state is inconsistent — defer .gitignore
+    // until next clean run). Resolve the effective repo path so the wire-up
+    // fires in the common case where the user runs `gbrain sync` without
+    // passing --repo every time.
+    if (result.status !== 'dry_run' && result.status !== 'blocked_by_failures') {
+      const effectiveRepoPath = opts.repoPath ?? (await getDefaultSourcePath(engine));
+      if (effectiveRepoPath) {
+        manageGitignore(effectiveRepoPath, engine.kind);
+      }
+    }
     return;
   }
 
@@ -865,6 +1090,14 @@ export async function runSync(engine: BrainEngine, args: string[]) {
         const ts = new Date().toISOString().slice(11, 19);
         console.log(`[${ts}] Synced: +${result.added} ~${result.modified} -${result.deleted} R${result.renamed}`);
       }
+      // Same gate as non-watch: only manage .gitignore on successful sync.
+      // Same repo-resolution path so watch mode catches the implicit-resolved case.
+      if (result.status !== 'dry_run' && result.status !== 'blocked_by_failures') {
+        const effectiveRepoPath = opts.repoPath ?? (await getDefaultSourcePath(engine));
+        if (effectiveRepoPath) {
+          manageGitignore(effectiveRepoPath, engine.kind);
+        }
+      }
     } catch (e: unknown) {
       consecutiveErrors++;
       const msg = e instanceof Error ? e.message : String(e);
@@ -878,6 +1111,124 @@ export async function runSync(engine: BrainEngine, args: string[]) {
   }
 }
 
+/**
+ * Auto-manage .gitignore entries for db_only directories.
+ *
+ * Caller invokes ONLY on successful sync — this function trusts that the
+ * sync's data state is consistent. See `runSync` for the gating logic.
+ *
+ * Idempotent: re-running adds no duplicate entries. The managed block has
+ * a stable comment header so it's grep-able and editable.
+ *
+ * Skipped (with actionable warning) when:
+ *   - GBRAIN_NO_GITIGNORE=1 — D23 escape hatch for shared-repo setups
+ *   - The repo is a git submodule (`.git` is a file not a directory) —
+ *     D49 lock; submodule .gitignore changes don't survive parent updates
+ *
+ * On PGLite (D4): emits a once-per-process soft-warn explaining that
+ * tiering has limited effect — but still manages the .gitignore so the
+ * config-present user gets the gitignore housekeeping.
+ *
+ * Failures (write permission denied, EROFS, etc.) are caught, warned, and
+ * swallowed (D9 lock). Sync's primary job is moving data; .gitignore
+ * management is a side effect — don't kill the main job for the side effect.
+ */
+let _pgliteTierWarned = false;
+export function __resetPGLiteTierWarn(): void {
+  _pgliteTierWarned = false;
+}
+
+export function manageGitignore(
+  repoPath: string,
+  engineKind?: 'pglite' | 'postgres',
+): void {
+  if (process.env.GBRAIN_NO_GITIGNORE === '1') {
+    return;
+  }
+
+  // D49: submodule detection. In a submodule, `.git` is a regular file
+  // (containing `gitdir: ../path/to/parent.git/modules/x`), not a directory.
+  const dotGit = join(repoPath, '.git');
+  if (existsSync(dotGit)) {
+    try {
+      if (statSync(dotGit).isFile()) {
+        console.warn(
+          `Note: skipping .gitignore management — ${repoPath} is a git submodule. ` +
+            `Add db_only directories to your parent repo's .gitignore manually.`,
+        );
+        return;
+      }
+    } catch {
+      // proceed; can't tell, default to managing
+    }
+  }
+
+  let storageConfig;
+  try {
+    storageConfig = loadStorageConfig(repoPath);
+  } catch (error) {
+    // StorageConfigError (overlap) or read error — surface, don't manage.
+    console.warn(
+      `Skipped .gitignore update: ${error instanceof Error ? error.message : String(error)}`,
+    );
+    return;
+  }
+  if (!storageConfig || storageConfig.db_only.length === 0) {
+    return;
+  }
+
+  // D4 soft-warn: storage tiering has limited effect on PGLite, but the
+  // .gitignore housekeeping still helps. Warn once per process; proceed.
+  if (engineKind === 'pglite' && !_pgliteTierWarned) {
+    _pgliteTierWarned = true;
+    console.warn(
+      `Note: storage tiering has limited effect on PGLite — pages live in your ` +
+        `local database file regardless of tier. Managing .gitignore anyway.`,
+    );
+  }
+
+  const gitignorePath = join(repoPath, '.gitignore');
+  let gitignoreContent = '';
+
+  if (existsSync(gitignorePath)) {
+    try {
+      gitignoreContent = readFileSync(gitignorePath, 'utf-8');
+    } catch (error) {
+      console.warn(
+        `Could not read ${gitignorePath} (${error instanceof Error ? error.message : String(error)}) — ` +
+          `skipping .gitignore update. Add db_only directories manually.`,
+      );
+      return;
+    }
+  }
+
+  const existingLines = new Set(gitignoreContent.split('\n').map((line) => line.trim()));
+  const linesToAdd: string[] = [];
+
+  for (const dir of storageConfig.db_only) {
+    if (!existingLines.has(dir) && !existingLines.has(`/${dir}`)) {
+      linesToAdd.push(dir);
+    }
+  }
+
+  if (linesToAdd.length === 0) return;
+
+  if (gitignoreContent && !gitignoreContent.endsWith('\n')) {
+    gitignoreContent += '\n';
+  }
+  gitignoreContent += '\n# Auto-managed by gbrain (db_only directories)\n';
+  gitignoreContent += linesToAdd.join('\n') + '\n';
+
+  try {
+    writeFileSync(gitignorePath, gitignoreContent);
+  } catch (error) {
+    console.warn(
+      `Could not update ${gitignorePath} (${error instanceof Error ? error.message : String(error)}) — ` +
+        `please add db_only directories manually:\n  ${linesToAdd.join('\n  ')}`,
+    );
+  }
+}
+
 function printSyncResult(result: SyncResult) {
   switch (result.status) {
     case 'up_to_date':

src/core/db-lock.ts

@@ -0,0 +1,140 @@
+/**
+ * Generic DB-backed lock primitive.
+ *
+ * Reuses the gbrain_cycle_locks table (id PK + holder_pid + ttl_expires_at)
+ * with a parameterized lock id. Both `gbrain-cycle` (the broad cycle lock)
+ * and `gbrain-sync` (performSync's writer lock) live here.
+ *
+ * Why not pg_advisory_xact_lock: it is session-scoped, and PgBouncer
+ * transaction pooling drops session state between calls. This row-based
+ * lock survives PgBouncer because it's plain INSERT/UPDATE/DELETE with
+ * a TTL fallback (a crashed holder's row times out).
+ *
+ * Why a separate table-row per lock id rather than reusing the cycle lock:
+ * the cycle lock is broader (covers every phase). performSync's write-window
+ * is narrower. If performSync reused the cycle lock and the cycle handler
+ * called performSync, the inner acquire would deadlock against itself. Two
+ * lock ids let callers nest cleanly: cycle holds gbrain-cycle for its run;
+ * performSync (called from anywhere — cycle, jobs handler, CLI) takes
+ * gbrain-sync just for the write window.
+ *
+ * v0.22.13 — added in PR #490 to fix CODEX-2 (no cross-process lock for
+ * direct sync paths). The cycle path was already protected.
+ */
+import { hostname } from 'os';
+import type { BrainEngine } from './engine.ts';
+
+export interface DbLockHandle {
+  id: string;
+  release: () => Promise<void>;
+  refresh: () => Promise<void>;
+}
+
+/** Default TTL: 30 minutes, same as cycle lock. */
+const DEFAULT_TTL_MINUTES = 30;
+
+/**
+ * Try to acquire a named DB lock.
+ *
+ * Returns a handle on success. Returns `null` if another live holder has
+ * the lock (its row exists and ttl_expires_at is in the future).
+ *
+ * The acquire is upsert-style:
+ *   INSERT ... ON CONFLICT (id) DO UPDATE
+ *     ... WHERE existing.ttl_expires_at < NOW()
+ *   RETURNING id
+ *
+ * Empty RETURNING means the existing row is still live. An expired holder
+ * (worker crashed without releasing) is auto-superseded by the UPDATE
+ * branch.
+ */
+export async function tryAcquireDbLock(
+  engine: BrainEngine,
+  lockId: string,
+  ttlMinutes: number = DEFAULT_TTL_MINUTES,
+): Promise<DbLockHandle | null> {
+  const pid = process.pid;
+  const host = hostname();
+
+  // Engine-agnostic: prefer the engine's raw escape hatch (`sql` for postgres-js,
+  // `db.query` for PGLite). Mirrors cycle.ts's pattern so behavior stays identical.
+  const maybePG = engine as unknown as { sql?: (...args: unknown[]) => Promise<unknown> };
+  const maybePGLite = engine as unknown as {
+    db?: { query: (sql: string, params?: unknown[]) => Promise<{ rows: unknown[] }> };
+  };
+
+  if (engine.kind === 'postgres' && maybePG.sql) {
+    const sql = maybePG.sql as any;
+    const ttl = `${ttlMinutes} minutes`;
+    const rows: Array<{ id: string }> = await sql`
+      INSERT INTO gbrain_cycle_locks (id, holder_pid, holder_host, acquired_at, ttl_expires_at)
+      VALUES (${lockId}, ${pid}, ${host}, NOW(), NOW() + ${ttl}::interval)
+      ON CONFLICT (id) DO UPDATE
+        SET holder_pid = ${pid},
+            holder_host = ${host},
+            acquired_at = NOW(),
+            ttl_expires_at = NOW() + ${ttl}::interval
+        WHERE gbrain_cycle_locks.ttl_expires_at < NOW()
+      RETURNING id
+    `;
+    if (rows.length === 0) return null;
+    return {
+      id: lockId,
+      refresh: async () => {
+        await sql`
+          UPDATE gbrain_cycle_locks
+            SET ttl_expires_at = NOW() + ${ttl}::interval
+          WHERE id = ${lockId} AND holder_pid = ${pid}
+        `;
+      },
+      release: async () => {
+        await sql`
+          DELETE FROM gbrain_cycle_locks
+          WHERE id = ${lockId} AND holder_pid = ${pid}
+        `;
+      },
+    };
+  }
+
+  if (engine.kind === 'pglite' && maybePGLite.db) {
+    const db = maybePGLite.db;
+    const ttl = `${ttlMinutes} minutes`;
+    const { rows } = await db.query(
+      `INSERT INTO gbrain_cycle_locks (id, holder_pid, holder_host, acquired_at, ttl_expires_at)
+       VALUES ($1, $2, $3, NOW(), NOW() + $4::interval)
+       ON CONFLICT (id) DO UPDATE
+         SET holder_pid = $2,
+             holder_host = $3,
+             acquired_at = NOW(),
+             ttl_expires_at = NOW() + $4::interval
+         WHERE gbrain_cycle_locks.ttl_expires_at < NOW()
+       RETURNING id`,
+      [lockId, pid, host, ttl],
+    );
+    if (rows.length === 0) return null;
+    return {
+      id: lockId,
+      refresh: async () => {
+        await db.query(
+          `UPDATE gbrain_cycle_locks
+              SET ttl_expires_at = NOW() + $1::interval
+            WHERE id = $2 AND holder_pid = $3`,
+          [ttl, lockId, pid],
+        );
+      },
+      release: async () => {
+        await db.query(
+          `DELETE FROM gbrain_cycle_locks WHERE id = $1 AND holder_pid = $2`,
+          [lockId, pid],
+        );
+      },
+    };
+  }
+
+  throw new Error(`Unknown engine kind for db-lock: ${engine.kind}`);
+}
+
+/** Lock id for performSync's writer window. Distinct from gbrain-cycle so the
+ * cycle handler can hold gbrain-cycle while performSync (called from inside
+ * the cycle) acquires gbrain-sync. */
+export const SYNC_LOCK_ID = 'gbrain-sync';

src/core/disk-walk.ts

@@ -0,0 +1,83 @@
+/**
+ * Recursive filesystem walk into a slug → Stats map.
+ *
+ * Replaces per-page `existsSync` + `statSync` syscall storms (Issue #14 of
+ * the v0.22.3 eng review). On a 200K-page brain the per-page approach was
+ * 400K syscalls in a synchronous loop; this walk is one syscall per directory
+ * plus one stat per file, then O(1) Map lookups for everything downstream.
+ *
+ * The slug key is the on-disk path relative to the brain repo, with the
+ * trailing `.md` stripped, matching how pages are stored: `people/alice.md`
+ * on disk becomes `people/alice` as a slug.
+ *
+ * Skipped entries:
+ *   - `.git/`, `node_modules/`, and dot-directories generally — not part of
+ *     the brain's page namespace. Speeds up walks significantly on dirty
+ *     working copies.
+ *   - Files that don't end in `.md`. Sidecar JSON, raw binary attachments,
+ *     etc. are tracked by the brain but not via slugs.
+ */
+
+import { readdirSync, statSync, type Stats, type Dirent } from 'fs';
+import { join } from 'path';
+
+export interface DiskFileEntry {
+  size: number;
+  mtimeMs: number;
+}
+
+/**
+ * Walk `repoPath` and return a Map of slug → file metadata for every `.md`
+ * file. Skips dot-directories. Synchronous (matches the call-site shape and
+ * the io pattern of stat-heavy scans).
+ *
+ * @param repoPath  Absolute path to the brain repo root.
+ * @returns  Map keyed by slug (no `.md` suffix). Empty map if repoPath
+ *           doesn't exist or contains no markdown files.
+ */
+export function walkBrainRepo(repoPath: string): Map<string, DiskFileEntry> {
+  const result = new Map<string, DiskFileEntry>();
+
+  function recurse(dirPath: string, slugPrefix: string): void {
+    // Annotate as Dirent[] explicitly: ReturnType<typeof readdirSync> with
+    // withFileTypes:true picks an overload union that includes
+    // Dirent<Buffer<ArrayBufferLike>>, which makes entry.name a Buffer in
+    // strict tsc mode. Cast to the string-based Dirent[] (same shape sync.ts
+    // uses for its own filesystem walk).
+    let entries: Dirent[];
+    try {
+      entries = readdirSync(dirPath, { withFileTypes: true }) as unknown as Dirent[];
+    } catch {
+      return; // unreadable directory — skip silently
+    }
+
+    for (const entry of entries) {
+      // Skip dot-directories (.git, .gbrain, .vscode, etc) and node_modules.
+      if (entry.name.startsWith('.') || entry.name === 'node_modules') continue;
+      const childPath = join(dirPath, entry.name);
+
+      if (entry.isDirectory()) {
+        recurse(childPath, slugPrefix ? `${slugPrefix}/${entry.name}` : entry.name);
+        continue;
+      }
+
+      if (!entry.isFile()) continue;
+      if (!entry.name.endsWith('.md')) continue;
+
+      let stats: Stats;
+      try {
+        stats = statSync(childPath);
+      } catch {
+        continue; // race: file deleted between readdir and stat
+      }
+
+      const slug = slugPrefix
+        ? `${slugPrefix}/${entry.name.slice(0, -3)}`
+        : entry.name.slice(0, -3);
+      result.set(slug, { size: stats.size, mtimeMs: stats.mtimeMs });
+    }
+  }
+
+  recurse(repoPath, '');
+  return result;
+}

src/core/migrate.ts

@@ -811,6 +811,14 @@ export const MIGRATIONS: Migration[] = [
         RAISE NOTICE 'v24: RLS backfill complete (role % has BYPASSRLS)', current_user;
       END $$;
     `,
+    // PGLite has no RLS engine and is intrinsically single-tenant (local file).
+    // The 8 ALTER TABLE ... ENABLE ROW LEVEL SECURITY statements above also
+    // target tables that may not exist on PGLite (subagent_*, minion_inbox),
+    // since pglite-schema.ts is the canonical PGLite schema source. No-op
+    // override keeps PGLite upgrades unwedged and the version bump intact.
+    sqlFor: {
+      pglite: '',
+    },
   },
   {
     version: 25,

src/core/pglite-engine.ts

@@ -86,6 +86,16 @@ export class PGLiteEngine implements BrainEngine {
   }
 
   async initSchema(): Promise<void> {
+    // Pre-schema bootstrap: add forward-referenced state the embedded schema
+    // blob requires but that older brains don't have yet. Without this, a
+    // pre-v0.18 brain hits `CREATE INDEX idx_pages_source_id ON pages(source_id)`
+    // (issues #366/#375/#378/#396) or a pre-v0.13 brain hits
+    // `CREATE INDEX idx_links_source ON links(link_source)` (#266/#357), and
+    // initSchema crashes before runMigrations gets a chance to apply the
+    // missing column. Bootstrap is structurally idempotent and a no-op on
+    // fresh installs and modern brains.
+    await this.applyForwardReferenceBootstrap();
+
     await this.db.exec(PGLITE_SCHEMA_SQL);
 
     const { applied } = await runMigrations(this);
@@ -94,6 +104,111 @@ export class PGLiteEngine implements BrainEngine {
     }
   }
 
+  /**
+   * Bootstrap state that PGLITE_SCHEMA_SQL forward-references but that older
+   * brains don't have yet. Currently covers:
+   *
+   *   - `sources` table + default seed (FK target of pages.source_id) — v0.18
+   *   - `pages.source_id` column (indexed by `idx_pages_source_id`) — v0.18
+   *   - `links.link_source` column (indexed by `idx_links_source`) — v0.13
+   *   - `links.origin_page_id` column (indexed by `idx_links_origin`) — v0.13
+   *   - `content_chunks.symbol_name` column (indexed by `idx_chunks_symbol_name`) — v0.19
+   *   - `content_chunks.language` column (indexed by `idx_chunks_language`) — v0.19
+   *
+   * **Maintenance contract:** when a future migration adds a column-with-index
+   * or new-table-with-FK referenced by PGLITE_SCHEMA_SQL, extend this method
+   * AND `test/schema-bootstrap-coverage.test.ts`'s `REQUIRED_BOOTSTRAP_COVERAGE`.
+   * The coverage test fails loudly if the bootstrap drifts behind the schema.
+   */
+  private async applyForwardReferenceBootstrap(): Promise<void> {
+    // Single round-trip probe for every forward-reference target.
+    const { rows } = await this.db.query(`
+      SELECT
+        EXISTS (SELECT 1 FROM information_schema.tables
+                WHERE table_schema='public' AND table_name='pages') AS pages_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema='public' AND table_name='pages' AND column_name='source_id') AS source_id_exists,
+        EXISTS (SELECT 1 FROM information_schema.tables
+                WHERE table_schema='public' AND table_name='links') AS links_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema='public' AND table_name='links' AND column_name='link_source') AS link_source_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema='public' AND table_name='links' AND column_name='origin_page_id') AS origin_page_id_exists,
+        EXISTS (SELECT 1 FROM information_schema.tables
+                WHERE table_schema='public' AND table_name='content_chunks') AS chunks_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema='public' AND table_name='content_chunks' AND column_name='symbol_name') AS symbol_name_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema='public' AND table_name='content_chunks' AND column_name='language') AS language_exists
+    `);
+    const probe = rows[0] as {
+      pages_exists: boolean;
+      source_id_exists: boolean;
+      links_exists: boolean;
+      link_source_exists: boolean;
+      origin_page_id_exists: boolean;
+      chunks_exists: boolean;
+      symbol_name_exists: boolean;
+      language_exists: boolean;
+    };
+
+    const needsPagesBootstrap = probe.pages_exists && !probe.source_id_exists;
+    const needsLinksBootstrap = probe.links_exists
+      && (!probe.link_source_exists || !probe.origin_page_id_exists);
+    const needsChunksBootstrap = probe.chunks_exists
+      && (!probe.symbol_name_exists || !probe.language_exists);
+
+    // Fresh installs (no tables yet) and modern brains both no-op.
+    if (!needsPagesBootstrap && !needsLinksBootstrap && !needsChunksBootstrap) return;
+
+    console.log('  Pre-v0.21 brain detected, applying forward-reference bootstrap');
+
+    if (needsPagesBootstrap) {
+      // Mirror schema-embedded.ts shape for `sources` so the subsequent
+      // PGLITE_SCHEMA_SQL CREATE TABLE IF NOT EXISTS is a true no-op.
+      await this.db.exec(`
+        CREATE TABLE IF NOT EXISTS sources (
+          id            TEXT PRIMARY KEY,
+          name          TEXT NOT NULL UNIQUE,
+          local_path    TEXT,
+          last_commit   TEXT,
+          last_sync_at  TIMESTAMPTZ,
+          config        JSONB NOT NULL DEFAULT '{}'::jsonb,
+          created_at    TIMESTAMPTZ NOT NULL DEFAULT now()
+        );
+        INSERT INTO sources (id, name, config)
+          VALUES ('default', 'default', '{"federated": true}'::jsonb)
+          ON CONFLICT (id) DO NOTHING;
+        ALTER TABLE pages ADD COLUMN IF NOT EXISTS source_id TEXT
+          NOT NULL DEFAULT 'default' REFERENCES sources(id) ON DELETE CASCADE;
+      `);
+    }
+
+    if (needsLinksBootstrap) {
+      // v11 (links_provenance_columns) is responsible for the CHECK constraint
+      // and backfill. The bootstrap only adds enough state for SCHEMA_SQL's
+      // `CREATE INDEX idx_links_source/origin` not to crash. v11 runs later
+      // via runMigrations and is idempotent (`IF NOT EXISTS` everywhere).
+      await this.db.exec(`
+        ALTER TABLE links ADD COLUMN IF NOT EXISTS link_source TEXT;
+        ALTER TABLE links ADD COLUMN IF NOT EXISTS origin_page_id INTEGER
+          REFERENCES pages(id) ON DELETE SET NULL;
+      `);
+    }
+
+    if (needsChunksBootstrap) {
+      // v26 (content_chunks_code_metadata) adds the full code-chunk metadata
+      // surface (language, symbol_name, symbol_type, start_line, end_line).
+      // The bootstrap only adds the two columns the schema blob's partial
+      // indexes reference (idx_chunks_symbol_name, idx_chunks_language).
+      // v26 runs later via runMigrations and adds the rest idempotently.
+      await this.db.exec(`
+        ALTER TABLE content_chunks ADD COLUMN IF NOT EXISTS language TEXT;
+        ALTER TABLE content_chunks ADD COLUMN IF NOT EXISTS symbol_name TEXT;
+      `);
+    }
+  }
+
   async withReservedConnection<T>(fn: (conn: ReservedConnection) => Promise<T>): Promise<T> {
     // PGLite has no connection pool. The single backing connection is
     // always effectively reserved — pass it through.
@@ -179,6 +294,13 @@ export class PGLiteEngine implements BrainEngine {
       params.push(filters.updated_after);
       where.push(`p.updated_at > $${params.length}::timestamptz`);
     }
+    // slugPrefix uses the (source_id, slug) UNIQUE btree for index range scans.
+    // Escape LIKE metacharacters so the user prefix is treated as a literal.
+    if (filters?.slugPrefix) {
+      const escaped = filters.slugPrefix.replace(/[\\%_]/g, (c) => '\\' + c) + '%';
+      params.push(escaped);
+      where.push(`p.slug LIKE $${params.length} ESCAPE '\\'`);
+    }
 
     const whereSql = where.length > 0 ? `WHERE ${where.join(' AND ')}` : '';
     params.push(limit, offset);

src/core/postgres-engine.ts

@@ -99,9 +99,26 @@ export class PostgresEngine implements BrainEngine {
   async initSchema(): Promise<void> {
     const conn = this.sql;
     // Advisory lock prevents concurrent initSchema() calls from deadlocking
-    // on DDL statements (DROP TRIGGER + CREATE TRIGGER acquire AccessExclusiveLock)
+    // on DDL statements (DROP TRIGGER + CREATE TRIGGER acquire AccessExclusiveLock).
+    //
+    // Honest limitation: pg_advisory_lock(42) is session-scoped to this pooled
+    // connection. runMigrations() below uses engine.transaction() and
+    // withReservedConnection() which may hop to a different backend in the
+    // pool. Cross-process serialization of initSchema is best-effort, not a
+    // correctness guarantee. Pre-existing concern; the bootstrap doesn't
+    // change it.
     await conn`SELECT pg_advisory_lock(42)`;
     try {
+      // Pre-schema bootstrap: add forward-referenced state the embedded schema
+      // blob requires but that older brains don't have yet. Without this, a
+      // pre-v0.18 brain hits `CREATE INDEX idx_pages_source_id ON pages(source_id)`
+      // (issues #366/#375/#378/#396), or a pre-v0.13 brain hits
+      // `CREATE INDEX idx_links_source ON links(link_source)` (#266/#357), and
+      // SCHEMA_SQL crashes before runMigrations gets a chance to apply the
+      // missing column. Bootstrap is structurally idempotent and a no-op on
+      // fresh installs and modern brains.
+      await this.applyForwardReferenceBootstrap();
+
       await conn.unsafe(SCHEMA_SQL);
 
       // Run any pending migrations automatically
@@ -122,6 +139,113 @@ export class PostgresEngine implements BrainEngine {
     }
   }
 
+  /**
+   * Bootstrap state that SCHEMA_SQL forward-references but that older brains
+   * don't have yet. Mirror of `PGLiteEngine#applyForwardReferenceBootstrap`
+   * in shape and intent. Currently covers:
+   *
+   *   - `sources` table + default seed (FK target of pages.source_id) — v0.18
+   *   - `pages.source_id` column (indexed by `idx_pages_source_id`) — v0.18
+   *   - `links.link_source` column (indexed by `idx_links_source`) — v0.13
+   *   - `links.origin_page_id` column (indexed by `idx_links_origin`) — v0.13
+   *   - `content_chunks.symbol_name` column (indexed by `idx_chunks_symbol_name`) — v0.19
+   *   - `content_chunks.language` column (indexed by `idx_chunks_language`) — v0.19
+   *
+   * Keep this in sync with the PGLite version; covered by
+   * `test/schema-bootstrap-coverage.test.ts` (PGLite side) and
+   * `test/e2e/postgres-bootstrap.test.ts` (Postgres side).
+   */
+  private async applyForwardReferenceBootstrap(): Promise<void> {
+    const conn = this.sql;
+
+    // Single round-trip probe for every forward-reference target.
+    // current_schema() resolves to whatever search_path the connection uses,
+    // which matches schema-embedded.ts's `public.` references.
+    const probeRows = await conn<{
+      pages_exists: boolean;
+      source_id_exists: boolean;
+      links_exists: boolean;
+      link_source_exists: boolean;
+      origin_page_id_exists: boolean;
+      chunks_exists: boolean;
+      symbol_name_exists: boolean;
+      language_exists: boolean;
+    }[]>`
+      SELECT
+        EXISTS (SELECT 1 FROM information_schema.tables
+                WHERE table_schema = current_schema() AND table_name = 'pages') AS pages_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema = current_schema() AND table_name = 'pages' AND column_name = 'source_id') AS source_id_exists,
+        EXISTS (SELECT 1 FROM information_schema.tables
+                WHERE table_schema = current_schema() AND table_name = 'links') AS links_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema = current_schema() AND table_name = 'links' AND column_name = 'link_source') AS link_source_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema = current_schema() AND table_name = 'links' AND column_name = 'origin_page_id') AS origin_page_id_exists,
+        EXISTS (SELECT 1 FROM information_schema.tables
+                WHERE table_schema = current_schema() AND table_name = 'content_chunks') AS chunks_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema = current_schema() AND table_name = 'content_chunks' AND column_name = 'symbol_name') AS symbol_name_exists,
+        EXISTS (SELECT 1 FROM information_schema.columns
+                WHERE table_schema = current_schema() AND table_name = 'content_chunks' AND column_name = 'language') AS language_exists
+    `;
+    const probe = probeRows[0]!;
+
+    const needsPagesBootstrap = probe.pages_exists && !probe.source_id_exists;
+    const needsLinksBootstrap = probe.links_exists
+      && (!probe.link_source_exists || !probe.origin_page_id_exists);
+    const needsChunksBootstrap = probe.chunks_exists
+      && (!probe.symbol_name_exists || !probe.language_exists);
+
+    if (!needsPagesBootstrap && !needsLinksBootstrap && !needsChunksBootstrap) return;
+
+    console.log('  Pre-v0.21 brain detected, applying forward-reference bootstrap');
+
+    if (needsPagesBootstrap) {
+      // Mirror schema-embedded.ts's `sources` shape so the subsequent
+      // SCHEMA_SQL CREATE TABLE IF NOT EXISTS is a true no-op.
+      await conn.unsafe(`
+        CREATE TABLE IF NOT EXISTS sources (
+          id            TEXT PRIMARY KEY,
+          name          TEXT NOT NULL UNIQUE,
+          local_path    TEXT,
+          last_commit   TEXT,
+          last_sync_at  TIMESTAMPTZ,
+          config        JSONB NOT NULL DEFAULT '{}'::jsonb,
+          created_at    TIMESTAMPTZ NOT NULL DEFAULT now()
+        );
+        INSERT INTO sources (id, name, config)
+          VALUES ('default', 'default', '{"federated": true}'::jsonb)
+          ON CONFLICT (id) DO NOTHING;
+        ALTER TABLE pages ADD COLUMN IF NOT EXISTS source_id TEXT
+          NOT NULL DEFAULT 'default' REFERENCES sources(id) ON DELETE CASCADE;
+      `);
+    }
+
+    if (needsLinksBootstrap) {
+      // v11 (links_provenance_columns) handles the CHECK constraint, the
+      // UNIQUE swap, and the backfill. The bootstrap only adds enough state
+      // for SCHEMA_SQL's `CREATE INDEX idx_links_source/origin` not to crash.
+      // v11 runs later via runMigrations and is idempotent.
+      await conn.unsafe(`
+        ALTER TABLE links ADD COLUMN IF NOT EXISTS link_source TEXT;
+        ALTER TABLE links ADD COLUMN IF NOT EXISTS origin_page_id INTEGER
+          REFERENCES pages(id) ON DELETE SET NULL;
+      `);
+    }
+
+    if (needsChunksBootstrap) {
+      // v26 (content_chunks_code_metadata) adds the full code-chunk metadata
+      // surface. The bootstrap only adds the two columns the schema blob's
+      // partial indexes reference (idx_chunks_symbol_name, idx_chunks_language).
+      // v26 runs later via runMigrations and adds the rest idempotently.
+      await conn.unsafe(`
+        ALTER TABLE content_chunks ADD COLUMN IF NOT EXISTS language TEXT;
+        ALTER TABLE content_chunks ADD COLUMN IF NOT EXISTS symbol_name TEXT;
+      `);
+    }
+  }
+
   async transaction<T>(fn: (engine: BrainEngine) => Promise<T>): Promise<T> {
     const conn = this._sql || db.getConnection();
     return conn.begin(async (tx) => {
@@ -210,11 +334,17 @@ export class PostgresEngine implements BrainEngine {
     const tagJoin = filters?.tag ? sql`JOIN tags t ON t.page_id = p.id` : sql``;
     const tagCondition = filters?.tag ? sql`AND t.tag = ${filters.tag}` : sql``;
     const updatedCondition = updatedAfter ? sql`AND p.updated_at > ${updatedAfter}::timestamptz` : sql``;
+    // slugPrefix uses the (source_id, slug) UNIQUE btree index for range scans.
+    // Escape LIKE metacharacters so the user prefix is treated as a literal.
+    const slugPrefix = filters?.slugPrefix;
+    const slugCondition = slugPrefix
+      ? sql`AND p.slug LIKE ${slugPrefix.replace(/[\\%_]/g, (c) => '\\' + c) + '%'} ESCAPE '\\'`
+      : sql``;
 
     const rows = await sql`
       SELECT p.* FROM pages p
       ${tagJoin}
-      WHERE 1=1 ${typeCondition} ${tagCondition} ${updatedCondition}
+      WHERE 1=1 ${typeCondition} ${tagCondition} ${updatedCondition} ${slugCondition}
       ORDER BY p.updated_at DESC LIMIT ${limit} OFFSET ${offset}
     `;
 

src/core/skillpack/installer.ts

@@ -183,7 +183,11 @@ function acquireLock(workspace: string, opts: InstallOptions): void {
   const existing = readLock(workspace);
   const staleMs = opts.lockStaleMs ?? DEFAULT_LOCK_STALE_MS;
   if (existing) {
-    const age = Date.now() - existing.mtimeMs;
+    // Clamp to 0. On Linux ext4, statSync().mtimeMs has sub-ms precision;
+    // Date.now() is integer ms. A file written microseconds ago can report
+    // a negative age here, which would break the staleMs:0 "any age is stale"
+    // contract the force-unlock path relies on (CI passes, local macOS masks it).
+    const age = Math.max(0, Date.now() - existing.mtimeMs);
     // `staleMs: 0` in tests means "any age counts as stale". Use >=
     // so a just-written lock qualifies when the threshold is 0.
     // Negative age (mtime in the future) happens on fast CI filesystems

src/core/source-resolver.ts

@@ -132,6 +132,42 @@ async function assertSourceExists(engine: BrainEngine, id: string): Promise<void
   }
 }
 
+/**
+ * Get the local_path of the resolved source (per the resolveSourceId chain).
+ *
+ * Returns the on-disk brain repo path for the source the user is currently
+ * operating against. Used by `gbrain storage status` and `gbrain export
+ * --restore-only` to find the brain repo without raw SQL or bare try/catch.
+ *
+ * Resolution order:
+ *   1. `sources.local_path` for the resolved source id (multi-source v0.18+ path)
+ *   2. Legacy global `sync.repo_path` config key (pre-v0.18 default-source brains)
+ *   3. null
+ *
+ * @returns local_path string, or null if no path is configured anywhere.
+ * @throws  If DB error occurs (does NOT silently swallow). Callers handle
+ *          the null case to provide their own fallback (typically a hard error
+ *          telling the user to pass --repo).
+ */
+export async function getDefaultSourcePath(
+  engine: BrainEngine,
+  cwd: string = process.cwd(),
+): Promise<string | null> {
+  const sourceId = await resolveSourceId(engine, null, cwd);
+  const rows = await engine.executeRaw<{ local_path: string | null }>(
+    `SELECT local_path FROM sources WHERE id = $1`,
+    [sourceId],
+  );
+  if (rows[0]?.local_path) return rows[0].local_path;
+
+  // Legacy fallback: pre-v0.18 brains stored the repo path in the global
+  // config table under sync.repo_path. The sources table exists but its
+  // local_path is NULL for the seeded 'default' row. Fall back so storage
+  // tiering works without forcing a `gbrain sources add . --path .` migration.
+  const legacyPath = await engine.getConfig('sync.repo_path');
+  return legacyPath ?? null;
+}
+
 /** Exposed for tests. */
 export const __testing = {
   readDotfileWalk,

src/core/storage-config.ts

@@ -0,0 +1,377 @@
+import { readFileSync, existsSync } from 'fs';
+import { join } from 'path';
+
+/**
+ * Storage tier configuration loaded from gbrain.yml.
+ *
+ * The canonical key names are `db_tracked` and `db_only` (engine-agnostic).
+ * The deprecated keys `git_tracked` and `supabase_only` are still read for
+ * backward compatibility but emit a once-per-process deprecation warning.
+ * Sunset: future release will reject the deprecated names.
+ */
+export interface StorageConfig {
+  db_tracked: string[];
+  db_only: string[];
+}
+
+export type StorageTier = 'db_tracked' | 'db_only' | 'unspecified';
+
+/** Recognized YAML keys (canonical and deprecated). */
+const STORAGE_KEYS = new Set([
+  'db_tracked', 'db_only',
+  'git_tracked', 'supabase_only', // deprecated aliases
+]);
+
+/**
+ * Parse the gbrain.yml shape: a top-level `storage:` section with up to four
+ * array-valued nested keys (canonical `db_tracked` / `db_only` plus the
+ * deprecated aliases `git_tracked` / `supabase_only`).
+ *
+ * Intentionally narrow. Does NOT handle the full YAML spec — only the file
+ * shape gbrain controls. Trades expressiveness for zero-dep parsing and
+ * predictable behavior. Returns null if the file has no `storage:` section
+ * (so callers can distinguish "no config" from "empty config").
+ *
+ * Replaces gray-matter, which silently returned `{data: {}}` on
+ * delimiter-less YAML and broke the entire feature on every install.
+ * The defect that prompted this rewrite: storage-config.ts:24 in the
+ * pre-v0.22.3 implementation.
+ *
+ * Returns the raw key map. The caller (loadStorageConfig) is responsible
+ * for normalizing deprecated keys → canonical, emitting deprecation
+ * warnings, and merging if both old and new keys appear.
+ */
+type RawStorage = {
+  db_tracked?: string[];
+  db_only?: string[];
+  git_tracked?: string[];
+  supabase_only?: string[];
+};
+
+function parseStorageYaml(content: string): RawStorage | null {
+  const lines = content.split('\n').map((line) => line.replace(/\r$/, ''));
+
+  let inStorage = false;
+  let currentList: keyof RawStorage | null = null;
+  const raw: RawStorage = {};
+  let sawStorage = false;
+
+  for (const line of lines) {
+    // Strip comments. Conservative: drop trailing `# ...` and full-line `#`.
+    const noComment = line.replace(/\s+#.*$/, '').replace(/^#.*$/, '');
+    if (noComment.trim() === '') continue;
+
+    // Top-level key (no leading whitespace).
+    if (!noComment.startsWith(' ') && !noComment.startsWith('\t')) {
+      const colon = noComment.indexOf(':');
+      if (colon === -1) continue;
+      const key = noComment.slice(0, colon).trim();
+      if (key === 'storage') {
+        inStorage = true;
+        sawStorage = true;
+        currentList = null;
+        continue;
+      }
+      inStorage = false;
+      currentList = null;
+      continue;
+    }
+
+    if (!inStorage) continue;
+
+    const indented = noComment.replace(/^\s+/, '');
+
+    if (indented.startsWith('-')) {
+      if (!currentList) continue;
+      const value = indented.slice(1).trim().replace(/^["']|["']$/g, '');
+      if (value) {
+        if (!raw[currentList]) raw[currentList] = [];
+        raw[currentList]!.push(value);
+      }
+      continue;
+    }
+
+    const colon = indented.indexOf(':');
+    if (colon === -1) continue;
+    const key = indented.slice(0, colon).trim();
+    if (STORAGE_KEYS.has(key)) {
+      currentList = key as keyof RawStorage;
+      // Inline empty list: `db_only: []`.
+      const remainder = indented.slice(colon + 1).trim();
+      if (remainder === '[]' && !raw[currentList]) {
+        raw[currentList] = [];
+      }
+      continue;
+    }
+    currentList = null;
+  }
+
+  if (!sawStorage) return null;
+  return raw;
+}
+
+/**
+ * Normalize raw parsed keys into canonical StorageConfig shape.
+ *
+ * Resolution order (per plan eng-review pass 2 finding #2):
+ *   1. If canonical keys present, use them.
+ *   2. Else if deprecated keys present, map to canonical AND emit a
+ *      once-per-process deprecation warning suggesting `gbrain doctor --fix`.
+ *   3. If both are present, canonical wins. Deprecated keys are ignored
+ *      with a stronger warning (the user is mid-migration).
+ *
+ * Validation (validateStorageConfig) always runs against the canonical
+ * shape, so error messages reference `db_only` / `db_tracked` regardless
+ * of which keys the user wrote.
+ */
+let _deprecationWarned = false;
+
+function normalizeStorageConfig(raw: RawStorage): StorageConfig {
+  const hasCanonical = Boolean(raw.db_tracked || raw.db_only);
+  const hasDeprecated = Boolean(raw.git_tracked || raw.supabase_only);
+
+  if (hasDeprecated && !_deprecationWarned) {
+    _deprecationWarned = true;
+    const which = [
+      raw.git_tracked ? '`git_tracked`' : null,
+      raw.supabase_only ? '`supabase_only`' : null,
+    ].filter(Boolean).join(' and ');
+    if (hasCanonical) {
+      console.warn(
+        `Warning: ${which} in gbrain.yml is deprecated and ignored ` +
+          `(canonical keys db_tracked/db_only are present). ` +
+          `Remove the deprecated keys, or run \`gbrain doctor --fix\`.`,
+      );
+    } else {
+      console.warn(
+        `Warning: ${which} in gbrain.yml is deprecated. ` +
+          `Rename to db_tracked / db_only — see docs/storage-tiering.md. ` +
+          `Run \`gbrain doctor --fix\` for an automated rename.`,
+      );
+    }
+  }
+
+  if (hasCanonical) {
+    return {
+      db_tracked: raw.db_tracked ?? [],
+      db_only: raw.db_only ?? [],
+    };
+  }
+
+  return {
+    db_tracked: raw.git_tracked ?? [],
+    db_only: raw.supabase_only ?? [],
+  };
+}
+
+/**
+ * Load gbrain.yml configuration from the brain repository root.
+ *
+ * Returns null when:
+ *   - repoPath is null/undefined
+ *   - gbrain.yml doesn't exist at the repo root
+ *   - gbrain.yml exists but has no `storage:` section (with sanity warning)
+ *
+ * Throws when:
+ *   - gbrain.yml exists but is unreadable (permission denied, etc.) — D36 lock:
+ *     fail loud rather than silently disable the feature.
+ *
+ * Logs a console.warn (once per process) when:
+ *   - File parses but `storage:` section is empty or missing — Issue #1 lock:
+ *     surface "your config didn't take" rather than silently no-op.
+ */
+let _missingStorageWarned = false;
+
+export function loadStorageConfig(repoPath?: string | null): StorageConfig | null {
+  if (!repoPath) return null;
+
+  const yamlPath = join(repoPath, 'gbrain.yml');
+  if (!existsSync(yamlPath)) return null;
+
+  // Read failure is a real error (not a "feature not configured" signal).
+  // Throwing here lets the caller decide whether to crash or fall back.
+  const content = readFileSync(yamlPath, 'utf-8');
+
+  let raw: RawStorage | null;
+  try {
+    raw = parseStorageYaml(content);
+  } catch (error) {
+    console.warn(
+      `Warning: Failed to parse gbrain.yml: ${error instanceof Error ? error.message : String(error)}`,
+    );
+    return null;
+  }
+
+  // No storage section at all → null (with sanity warning).
+  if (raw === null) {
+    if (!_missingStorageWarned) {
+      _missingStorageWarned = true;
+      console.warn(
+        `Warning: ${yamlPath} exists but has no storage configuration. ` +
+          `Add a "storage:" section with db_tracked / db_only arrays, ` +
+          `or remove gbrain.yml to suppress this warning.`,
+      );
+    }
+    return null;
+  }
+
+  const merged = normalizeStorageConfig(raw);
+
+  // Empty storage section → return as-is but warn.
+  if (merged.db_tracked.length === 0 && merged.db_only.length === 0) {
+    if (!_missingStorageWarned) {
+      _missingStorageWarned = true;
+      console.warn(
+        `Warning: ${yamlPath} exists but has no storage configuration. ` +
+          `Add a "storage:" section with db_tracked / db_only arrays, ` +
+          `or remove gbrain.yml to suppress this warning.`,
+      );
+    }
+    return merged;
+  }
+
+  // Normalize cosmetic issues + throw on semantic overlap (D7).
+  // Throws StorageConfigError on overlap — propagates to the caller.
+  return normalizeAndValidateStorageConfig(merged);
+}
+
+export class StorageConfigError extends Error {
+  constructor(message: string) {
+    super(message);
+    this.name = 'StorageConfigError';
+  }
+}
+
+/**
+ * Validate storage configuration for conflicts and issues.
+ * Returns warning strings; callers decide how to surface them.
+ *
+ * Always runs against the canonical (db_tracked / db_only) shape — error
+ * messages reference canonical names regardless of which keys the user
+ * wrote in gbrain.yml.
+ *
+ * Pure: does not mutate. For the auto-normalize behavior (D7), see
+ * `normalizeAndValidateStorageConfig` below.
+ */
+export function validateStorageConfig(config: StorageConfig): string[] {
+  const warnings: string[] = [];
+
+  const trackedSet = new Set(config.db_tracked);
+  for (const path of config.db_only) {
+    if (trackedSet.has(path)) {
+      warnings.push(`Directory "${path}" appears in both db_tracked and db_only`);
+    }
+  }
+
+  const allPaths = [...config.db_tracked, ...config.db_only];
+  for (const path of allPaths) {
+    if (!path.endsWith('/')) {
+      warnings.push(`Directory path "${path}" should end with "/" for consistency`);
+    }
+  }
+
+  return warnings;
+}
+
+/**
+ * Auto-normalize and strict-validate per D7+D8.
+ *
+ *   1. Cosmetic fixups are applied silently with a one-time info message
+ *      naming what changed:
+ *        - missing trailing `/` is added
+ *      The message helps the user learn the canonical form without nagging.
+ *   2. Semantic problems THROW (don't return warnings):
+ *        - same directory in both tiers (ambiguous routing)
+ *
+ * Caller passes a fresh raw config; this returns the normalized shape that
+ * the rest of the code (matcher, sync, etc.) sees.
+ */
+let _normalizationInfoEmitted = false;
+
+export function normalizeAndValidateStorageConfig(input: StorageConfig): StorageConfig {
+  const normalize = (paths: string[]): { normalized: string[]; changed: string[] } => {
+    const normalized: string[] = [];
+    const changed: string[] = [];
+    for (const p of paths) {
+      if (p.endsWith('/')) {
+        normalized.push(p);
+      } else {
+        normalized.push(p + '/');
+        changed.push(`"${p}" → "${p}/"`);
+      }
+    }
+    return { normalized, changed };
+  };
+
+  const tracked = normalize(input.db_tracked);
+  const dbonly = normalize(input.db_only);
+  const allChanged = [...tracked.changed, ...dbonly.changed];
+
+  if (allChanged.length > 0 && !_normalizationInfoEmitted) {
+    _normalizationInfoEmitted = true;
+    console.warn(
+      `Note: normalized ${allChanged.length} storage path(s) in gbrain.yml — ` +
+        `${allChanged.join(', ')}. Add trailing "/" to suppress this note.`,
+    );
+  }
+
+  // Semantic check: overlap between tiers throws. Ambiguous routing.
+  const trackedSet = new Set(tracked.normalized);
+  for (const path of dbonly.normalized) {
+    if (trackedSet.has(path)) {
+      throw new StorageConfigError(
+        `gbrain.yml: directory "${path}" appears in both db_tracked and db_only — ` +
+          `pick one tier. Edit gbrain.yml to remove the overlap.`,
+      );
+    }
+  }
+
+  return { db_tracked: tracked.normalized, db_only: dbonly.normalized };
+}
+
+/**
+ * Path-segment match: a slug belongs to a tier directory iff the directory
+ * is a complete path-segment ancestor of the slug. `media/x/` matches
+ * `media/x/foo` but NOT `media/xerox/foo` — eliminates the prefix-collision
+ * class of bug (Issue #5 of the eng review, D6 lock).
+ *
+ * Strict: requires the configured directory to end with `/`. The validator
+ * (per D7+D8) auto-normalizes input so the matcher only ever sees canonical
+ * trailing-`/` directories.
+ */
+function matchesTierDir(slug: string, dir: string): boolean {
+  if (!dir.endsWith('/')) return false; // not normalized — matcher refuses
+  // slug must equal dir's bare prefix OR start with the trailing-slash form.
+  // Example: dir = 'media/x/' matches 'media/x/anything' but not 'media/x'
+  // or 'media/xerox'. (A slug that exactly equals 'media/x' is a directory-
+  // level entry the brain doesn't write.)
+  return slug.startsWith(dir);
+}
+
+export function isDbTracked(slug: string, config: StorageConfig): boolean {
+  return config.db_tracked.some((dir) => matchesTierDir(slug, dir));
+}
+
+export function isDbOnly(slug: string, config: StorageConfig): boolean {
+  return config.db_only.some((dir) => matchesTierDir(slug, dir));
+}
+
+export function getStorageTier(slug: string, config: StorageConfig): StorageTier {
+  if (isDbTracked(slug, config)) return 'db_tracked';
+  if (isDbOnly(slug, config)) return 'db_only';
+  return 'unspecified';
+}
+
+// ── Deprecated aliases — to be removed in a future release ────────
+// Kept so existing callers (storage.ts, export.ts) compile during the
+// step-by-step refactor. Will be deleted once those call sites migrate
+// to the canonical names.
+export const isGitTracked = isDbTracked;
+export const isSupabaseOnly = isDbOnly;
+
+/** Reset once-per-process warning flags. Test-only. */
+export function __resetMissingStorageWarning(): void {
+  _missingStorageWarned = false;
+  _deprecationWarned = false;
+  _normalizationInfoEmitted = false;
+}

src/core/sync-concurrency.ts

@@ -0,0 +1,101 @@
+/**
+ * Shared concurrency policy for sync + import + jobs paths.
+ *
+ * Three callers used to embed three different policies:
+ *   - performSync (incremental): >100 files → 4 workers
+ *   - performFullSync: Postgres → 4 workers
+ *   - jobs.ts sync handler: hardcoded 4
+ *
+ * They drift over time and confuse users ("why does my sync not parallelize?"
+ * is a different answer in each path). This module is one source of truth.
+ *
+ * v0.22.13 — extracted as part of the parallel-sync hardening (PR #490).
+ */
+import type { BrainEngine } from './engine.ts';
+
+/** Threshold above which auto-concurrency fires for incremental sync paths. */
+export const AUTO_CONCURRENCY_FILE_THRESHOLD = 100;
+
+/** Minimum file count below which the parallel branch is skipped even when
+ * auto-concurrency would otherwise fire. Prevents spawning workers for trivial
+ * diffs where setup cost exceeds parallelism gains. Only consulted on the
+ * auto path; explicit `--workers N` bypasses this. */
+export const PARALLEL_FILE_FLOOR = 50;
+
+/** Default worker count when auto-concurrency fires. */
+export const DEFAULT_PARALLEL_WORKERS = 4;
+
+/**
+ * Resolve effective worker count for a sync/import operation.
+ *
+ * Inputs:
+ *   - engine.kind: 'pglite' always returns 1 (single-connection)
+ *   - override: caller's explicit --workers / opts.concurrency value
+ *   - fileCount: size of the work batch
+ *
+ * Rules:
+ *   - PGLite → always 1 (the engine is single-connection regardless)
+ *   - explicit override → respect it (clamped to >=1)
+ *   - auto path → DEFAULT_PARALLEL_WORKERS when fileCount > AUTO_CONCURRENCY_FILE_THRESHOLD, else 1
+ *
+ * Note: this function does NOT consult PARALLEL_FILE_FLOOR. The floor is a
+ * caller-side gate that decides whether to take the parallel code path even
+ * when the worker count is > 1. It only applies to the auto path; explicit
+ * --workers bypasses the floor entirely (per Q1 in PR #490).
+ */
+export function autoConcurrency(
+  engine: BrainEngine,
+  fileCount: number,
+  override?: number,
+): number {
+  if (engine.kind === 'pglite') return 1;
+  if (override !== undefined) return Math.max(1, override);
+  return fileCount > AUTO_CONCURRENCY_FILE_THRESHOLD
+    ? DEFAULT_PARALLEL_WORKERS
+    : 1;
+}
+
+/**
+ * Decide whether the parallel code path should run.
+ *
+ *   - workers <= 1 → never parallel
+ *   - workers > 1 + explicit override → always parallel (user opted in,
+ *     respect them even on small diffs — Q1 in PR #490)
+ *   - workers > 1 + auto path → parallel only when fileCount > PARALLEL_FILE_FLOOR
+ */
+export function shouldRunParallel(
+  workers: number,
+  fileCount: number,
+  explicit: boolean,
+): boolean {
+  if (workers <= 1) return false;
+  if (explicit) return true;
+  return fileCount > PARALLEL_FILE_FLOOR;
+}
+
+/**
+ * Parse a `--workers N` / `--concurrency N` CLI argument value.
+ *
+ * Returns:
+ *   - undefined when the flag was not provided
+ *   - a positive integer when the flag was provided with a valid value
+ *
+ * Throws on:
+ *   - non-integer ("foo", "1.5", "")
+ *   - zero or negative ("0", "-3")
+ *   - NaN / Infinity
+ *
+ * Q2 in PR #490: the prior parseInt-with-no-validation accepted `--workers 0`
+ * and silently fell through to auto-concurrency (4 workers), the opposite of
+ * what the user typed. Fail loud instead.
+ */
+export function parseWorkers(s: string | undefined): number | undefined {
+  if (s === undefined) return undefined;
+  const n = parseInt(s, 10);
+  if (!Number.isFinite(n) || n < 1 || String(n) !== s.trim()) {
+    throw new Error(
+      `--workers must be a positive integer, got: ${JSON.stringify(s)}`,
+    );
+  }
+  return n;
+}

src/core/sync.ts

@@ -307,6 +307,8 @@ import { createHash as _createHash } from 'crypto';
 export interface SyncFailure {
   path: string;
   error: string;
+  /** Structured error code extracted from the error message. */
+  code?: string;
   commit: string;
   line?: number;
   ts: string;
@@ -314,6 +316,91 @@ export interface SyncFailure {
   acknowledged_at?: string;
 }
 
+/**
+ * Best-effort extraction of a structured error code from a sync failure
+ * message. Matches known ParseValidationCode patterns (SLUG_MISMATCH,
+ * YAML_PARSE, etc.) and common DB / timeout errors. Returns 'UNKNOWN'
+ * when no pattern matches.
+ *
+ * Order matters: DB-layer errors are checked BEFORE YAML-layer ones so
+ * Postgres `duplicate key value violates unique constraint` doesn't get
+ * mislabeled as a YAML duplicate-key. Frontmatter patterns key off the
+ * canonical messages emitted by `collectValidationErrors()` in markdown.ts.
+ */
+export function classifyErrorCode(errorMsg: string): string {
+  // SLUG_MISMATCH: thrown by importFromFile() at src/core/import-file.ts:374.
+  if (/slug.*does not match|SLUG_MISMATCH/i.test(errorMsg)) return 'SLUG_MISMATCH';
+
+  // DB-layer errors come BEFORE the YAML duplicate-key check. Postgres unique-
+  // constraint violations contain "duplicate key" but are not a YAML problem.
+  if (/duplicate key value violates unique constraint|DB_DUPLICATE_KEY/i.test(errorMsg)) {
+    return 'DB_DUPLICATE_KEY';
+  }
+  if (/canceling statement due to statement timeout|STATEMENT_TIMEOUT/i.test(errorMsg)) {
+    return 'STATEMENT_TIMEOUT';
+  }
+
+  // YAML / frontmatter patterns. These match either the canonical message
+  // strings in src/core/markdown.ts (collectValidationErrors) or the literal
+  // ParseValidationCode token, so they fire whether the caller stores the
+  // message or just the code.
+  if (/YAML parse failed|YAML_PARSE/i.test(errorMsg)) return 'YAML_PARSE';
+  if (/YAMLException|duplicated mapping key|YAML_DUPLICATE_KEY/i.test(errorMsg)) {
+    return 'YAML_DUPLICATE_KEY';
+  }
+  if (/File is empty or whitespace-only|Frontmatter must start with ---|MISSING_OPEN/i.test(errorMsg)) {
+    return 'MISSING_OPEN';
+  }
+  if (/No closing --- delimiter|Heading at line .* found inside frontmatter|MISSING_CLOSE/i.test(errorMsg)) {
+    return 'MISSING_CLOSE';
+  }
+  if (/Frontmatter block is empty|EMPTY_FRONTMATTER/i.test(errorMsg)) return 'EMPTY_FRONTMATTER';
+  if (/Content contains null bytes|NULL_BYTES|null byte/i.test(errorMsg)) return 'NULL_BYTES';
+  if (/Nested double quotes|NESTED_QUOTES/i.test(errorMsg)) return 'NESTED_QUOTES';
+
+  // Generic fallbacks.
+  if (/invalid UTF-?8|INVALID_UTF8/i.test(errorMsg)) return 'INVALID_UTF8';
+
+  // v0.22.12 additions: covers the four real production sites in src/core/import-file.ts
+  // (lines 199, 347, 352, 401) that previously bucketed to UNKNOWN.
+  if (/file too large|content too large|FILE_TOO_LARGE/i.test(errorMsg)) return 'FILE_TOO_LARGE';
+  if (/skipping symlink|symlink|SYMLINK_NOT_ALLOWED/i.test(errorMsg)) return 'SYMLINK_NOT_ALLOWED';
+  return 'UNKNOWN';
+}
+
+/** Group failures by error code and return a sorted summary. */
+export function summarizeFailuresByCode(
+  failures: Array<{ error: string; code?: string }>,
+): Array<{ code: string; count: number }> {
+  const counts: Record<string, number> = {};
+  for (const f of failures) {
+    const code = f.code ?? classifyErrorCode(f.error);
+    counts[code] = (counts[code] ?? 0) + 1;
+  }
+  return Object.entries(counts)
+    .sort(([, a], [, b]) => b - a)
+    .map(([code, count]) => ({ code, count }));
+}
+
+/**
+ * Format a code-grouped summary as a human-readable multi-line string for
+ * stderr / doctor output. Accepts either raw failures (which are summarized
+ * internally) or an already-summarized `{code, count}[]` shape (the return
+ * value of `summarizeFailuresByCode` or `AcknowledgeResult.summary`).
+ * Returns an empty string when the input is empty.
+ */
+export function formatCodeBreakdown(
+  input: Array<{ error: string; code?: string }> | Array<{ code: string; count: number }>,
+): string {
+  // Distinguish by shape: summary entries have a numeric `count`. Empty array
+  // returns '' from either branch — both paths produce a 0-length join.
+  const summary =
+    input.length > 0 && typeof (input[0] as { count?: unknown }).count === 'number'
+      ? (input as Array<{ code: string; count: number }>)
+      : summarizeFailuresByCode(input as Array<{ error: string; code?: string }>);
+  return summary.map(s => `  ${s.code}: ${s.count}`).join('\n');
+}
+
 function _failuresDir(): string {
   return _joinPath(_homedir(), '.gbrain');
 }
@@ -370,6 +457,7 @@ export function recordSyncFailures(
     const entry: SyncFailure = {
       path: f.path,
       error: f.error,
+      code: classifyErrorCode(f.error),
       commit,
       line: f.line,
       ts: now,
@@ -380,28 +468,42 @@ export function recordSyncFailures(
   }
 }
 
+export interface AcknowledgeResult {
+  count: number;
+  summary: Array<{ code: string; count: number }>;
+}
+
 /**
  * Mark all unacknowledged failures as acknowledged. Used by
- * `gbrain sync --skip-failed`. Returns the number newly acknowledged.
+ * `gbrain sync --skip-failed`. Returns count and a structured summary
+ * grouped by error code so the operator can see *why* files were skipped.
  *
  * We do not delete — acknowledged entries stay as historical record so
  * doctor can still show them under a "previously skipped" bucket.
  */
-export function acknowledgeSyncFailures(): number {
+export function acknowledgeSyncFailures(): AcknowledgeResult {
   const entries = loadSyncFailures();
-  if (entries.length === 0) return 0;
+  if (entries.length === 0) return { count: 0, summary: [] };
   const now = new Date().toISOString();
   let changed = 0;
+  const newlyAcked: SyncFailure[] = [];
   const updated = entries.map(e => {
     if (e.acknowledged) return e;
     changed++;
-    return { ...e, acknowledged: true, acknowledged_at: now };
+    // Backfill code for entries that predate the code field.
+    const code = e.code ?? classifyErrorCode(e.error);
+    const acked = { ...e, code, acknowledged: true, acknowledged_at: now };
+    newlyAcked.push(acked);
+    return acked;
   });
-  if (changed === 0) return 0;
+  if (changed === 0) return { count: 0, summary: [] };
   _mkdirSync(_failuresDir(), { recursive: true });
   const fd = require('fs').writeFileSync;
   fd(syncFailuresPath(), updated.map(e => JSON.stringify(e)).join('\n') + '\n');
-  return changed;
+  return {
+    count: changed,
+    summary: summarizeFailuresByCode(newlyAcked),
+  };
 }
 
 /** Return only unacknowledged failures. */

src/core/types.ts

@@ -45,6 +45,14 @@ export interface PageFilters {
   offset?: number;
   /** ISO date string (YYYY-MM-DD or full ISO timestamp). Filter to pages updated_at > value. */
   updated_after?: string;
+  /**
+   * Prefix-match filter on slug. Implemented as `WHERE slug LIKE prefix || '%'`
+   * in both engines so it uses the (source_id, slug) UNIQUE constraint's btree
+   * index for efficient range scans on large brains. Used by storage-tiering
+   * commands (gbrain storage status, gbrain export --restore-only) to scope
+   * queries to a tier directory without loading every page into memory.
+   */
+  slugPrefix?: string;
 }
 
 // Chunks

src/mcp/dispatch.ts

@@ -0,0 +1,103 @@
+/**
+ * Shared MCP tool-call dispatch — single source of truth for stdio + HTTP transports.
+ *
+ * Both transports validate the same params, build the same OperationContext shape,
+ * and serialize errors identically. Drift between transports caused PR #483's reversed-args
+ * + missing-context bugs; this module exists to prevent that recurring.
+ */
+
+import type { BrainEngine } from '../core/engine.ts';
+import { operations, OperationError } from '../core/operations.ts';
+import type { Operation, OperationContext } from '../core/operations.ts';
+import { loadConfig } from '../core/config.ts';
+
+export interface ToolResult {
+  content: { type: 'text'; text: string }[];
+  isError?: boolean;
+}
+
+export interface DispatchOpts {
+  /** Defaults to true (remote/untrusted). Local CLI callers (`gbrain call`) pass false. */
+  remote?: boolean;
+  /** Override the default stderr logger (e.g. CLI uses console.* directly). */
+  logger?: OperationContext['logger'];
+}
+
+/** Validate required params exist and have the expected type. Returns null on success, error message on failure. */
+export function validateParams(op: Operation, params: Record<string, unknown>): string | null {
+  for (const [key, def] of Object.entries(op.params)) {
+    if (def.required && (params[key] === undefined || params[key] === null)) {
+      return `Missing required parameter: ${key}`;
+    }
+    if (params[key] !== undefined && params[key] !== null) {
+      const val = params[key];
+      const expected = def.type;
+      if (expected === 'string' && typeof val !== 'string') return `Parameter "${key}" must be a string`;
+      if (expected === 'number' && typeof val !== 'number') return `Parameter "${key}" must be a number`;
+      if (expected === 'boolean' && typeof val !== 'boolean') return `Parameter "${key}" must be a boolean`;
+      if (expected === 'object' && (typeof val !== 'object' || Array.isArray(val))) return `Parameter "${key}" must be an object`;
+      if (expected === 'array' && !Array.isArray(val)) return `Parameter "${key}" must be an array`;
+    }
+  }
+  return null;
+}
+
+const stderrLogger: OperationContext['logger'] = {
+  info: (msg: string) => process.stderr.write(`[info] ${msg}\n`),
+  warn: (msg: string) => process.stderr.write(`[warn] ${msg}\n`),
+  error: (msg: string) => process.stderr.write(`[error] ${msg}\n`),
+};
+
+export function buildOperationContext(
+  engine: BrainEngine,
+  params: Record<string, unknown>,
+  opts: DispatchOpts = {},
+): OperationContext {
+  return {
+    engine,
+    config: loadConfig() || { engine: 'postgres' },
+    logger: opts.logger || stderrLogger,
+    dryRun: !!params.dry_run,
+    remote: opts.remote ?? true,
+  };
+}
+
+/**
+ * Resolve operation, validate params, build context, invoke handler, format result.
+ *
+ * Returns a `ToolResult` with the same shape both MCP transports need:
+ * `{ content: [{ type: 'text', text }], isError?: boolean }`.
+ */
+export async function dispatchToolCall(
+  engine: BrainEngine,
+  name: string,
+  params: Record<string, unknown> | undefined,
+  opts: DispatchOpts = {},
+): Promise<ToolResult> {
+  const op = operations.find(o => o.name === name);
+  if (!op) {
+    return { content: [{ type: 'text', text: `Error: Unknown tool: ${name}` }], isError: true };
+  }
+
+  const safeParams = params || {};
+  const validationError = validateParams(op, safeParams);
+  if (validationError) {
+    return {
+      content: [{ type: 'text', text: JSON.stringify({ error: 'invalid_params', message: validationError }, null, 2) }],
+      isError: true,
+    };
+  }
+
+  const ctx = buildOperationContext(engine, safeParams, opts);
+
+  try {
+    const result = await op.handler(ctx, safeParams);
+    return { content: [{ type: 'text', text: JSON.stringify(result, null, 2) }] };
+  } catch (e: unknown) {
+    if (e instanceof OperationError) {
+      return { content: [{ type: 'text', text: JSON.stringify(e.toJSON(), null, 2) }], isError: true };
+    }
+    const msg = e instanceof Error ? e.message : String(e);
+    return { content: [{ type: 'text', text: `Error: ${msg}` }], isError: true };
+  }
+}

src/mcp/http-transport.ts

@@ -0,0 +1,354 @@
+/**
+ * HTTP transport for `gbrain serve --http`.
+ *
+ * Postgres-only. PGLite users get a clear fail-fast at startup (the access_tokens
+ * table doesn't exist on PGLite per pglite-schema.ts).
+ *
+ * Security model:
+ *   - Every request must include `Authorization: Bearer <token>` (except /health)
+ *   - Tokens are validated against SHA-256 hashes in the access_tokens table
+ *   - Create/manage tokens with auth.ts (gbrain auth create/list/revoke)
+ *   - No open OAuth, no client_credentials, no self-service tokens
+ *
+ * Hardening:
+ *   - CORS default-deny: allowlist via GBRAIN_HTTP_CORS_ORIGIN (comma-separated)
+ *   - Rate limit: per-IP pre-auth (protects DB from brute-force load) + per-token-id post-auth
+ *     (limits runaway clients). Default 30 req/min per IP, 60 req/min per token. Bounded LRU
+ *     so attacker-controlled keys can't grow memory unbounded.
+ *   - Body cap: 1 MiB default (GBRAIN_HTTP_MAX_BODY_BYTES). Stream-counted, not buffered —
+ *     chunked transfers without Content-Length are still capped.
+ *   - last_used_at debounce: only one UPDATE per token per 60s (SQL-level WHERE clause).
+ *   - mcp_request_log: one row per request with token_name + operation + status + latency.
+ *
+ * Replaces the standalone HTTP+OAuth wrapper that was vulnerable to unauthenticated
+ * client registration (see SECURITY.md).
+ */
+
+import { createHash } from 'crypto';
+import type { BrainEngine } from '../core/engine.ts';
+import { buildToolDefs } from './tool-defs.ts';
+import { operations } from '../core/operations.ts';
+import { VERSION } from '../version.ts';
+import { dispatchToolCall } from './dispatch.ts';
+import { buildDefaultLimiters, type RateLimiter } from './rate-limit.ts';
+
+const DEFAULT_BODY_CAP = 1024 * 1024; // 1 MiB
+
+function hashToken(token: string): string {
+  return createHash('sha256').update(token).digest('hex');
+}
+
+function envInt(name: string, fallback: number): number {
+  const v = process.env[name];
+  if (!v) return fallback;
+  const n = parseInt(v, 10);
+  return Number.isFinite(n) && n > 0 ? n : fallback;
+}
+
+function parseCorsAllowlist(): Set<string> | null {
+  const v = process.env.GBRAIN_HTTP_CORS_ORIGIN;
+  if (!v) return null;
+  return new Set(v.split(',').map(s => s.trim()).filter(Boolean));
+}
+
+interface HttpTransportOptions {
+  port: number;
+  engine: BrainEngine;
+  /** Override limiters (for tests). Defaults to env-driven buildDefaultLimiters. */
+  limiters?: { ip: RateLimiter; token: RateLimiter };
+}
+
+interface AuthResult {
+  ok: boolean;
+  tokenId?: string;
+  tokenName?: string;
+}
+
+/** Read up to `cap` bytes off req.body. Returns null if cap exceeded. */
+async function readBodyWithCap(req: Request, cap: number): Promise<string | null> {
+  const cl = req.headers.get('content-length');
+  if (cl) {
+    const n = parseInt(cl, 10);
+    if (Number.isFinite(n) && n > cap) return null;
+  }
+  const reader = req.body?.getReader();
+  if (!reader) return '';
+  const chunks: Uint8Array[] = [];
+  let total = 0;
+  while (true) {
+    const { value, done } = await reader.read();
+    if (done) break;
+    if (!value) continue;
+    total += value.byteLength;
+    if (total > cap) {
+      try { await reader.cancel(); } catch { /* noop */ }
+      return null;
+    }
+    chunks.push(value);
+  }
+  // Concatenate without Buffer to keep this Node-vs-Bun-portable.
+  const merged = new Uint8Array(total);
+  let offset = 0;
+  for (const c of chunks) {
+    merged.set(c, offset);
+    offset += c.byteLength;
+  }
+  return new TextDecoder().decode(merged);
+}
+
+/** Resolve client IP. Honors X-Forwarded-For only when GBRAIN_HTTP_TRUST_PROXY=1. */
+function resolveClientIp(req: Request, server: { requestIP: (r: Request) => { address: string } | null }): string {
+  if (process.env.GBRAIN_HTTP_TRUST_PROXY === '1') {
+    const xff = req.headers.get('x-forwarded-for');
+    if (xff) {
+      const first = xff.split(',')[0]?.trim();
+      if (first) return first;
+    }
+    const xRealIp = req.headers.get('x-real-ip');
+    if (xRealIp) return xRealIp.trim();
+  }
+  const sock = server.requestIP(req);
+  return sock?.address || 'unknown';
+}
+
+export async function startHttpTransport(opts: HttpTransportOptions) {
+  const { port, engine } = opts;
+
+  // Fail-fast: HTTP transport requires Postgres because access_tokens / mcp_request_log
+  // only exist in the Postgres schema (see src/core/pglite-schema.ts:5-6).
+  if ((engine as { kind?: string }).kind !== 'postgres') {
+    console.error('Error: gbrain serve --http requires a Postgres engine for remote auth tokens.');
+    console.error('PGLite is local-only by design (access_tokens table is Postgres-only).');
+    console.error('Either:');
+    console.error('  - Use stdio: gbrain serve');
+    console.error('  - Migrate to Postgres: gbrain migrate --to supabase');
+    process.exit(1);
+  }
+
+  const sql = (engine as unknown as { sql: any }).sql;
+  if (!sql) {
+    console.error('Error: Postgres engine has no .sql client. Engine may not be connected.');
+    process.exit(1);
+  }
+
+  const limiters = opts.limiters || buildDefaultLimiters();
+  const bodyCap = envInt('GBRAIN_HTTP_MAX_BODY_BYTES', DEFAULT_BODY_CAP);
+  const corsAllowlist = parseCorsAllowlist();
+  const tools = buildToolDefs(operations);
+
+  function corsHeaders(origin: string | null, extra: Record<string, string> = {}): Record<string, string> {
+    const headers: Record<string, string> = { ...extra };
+    if (corsAllowlist && origin && corsAllowlist.has(origin)) {
+      headers['Access-Control-Allow-Origin'] = origin;
+      headers['Vary'] = 'Origin';
+    }
+    return headers;
+  }
+
+  function corsPreflightHeaders(origin: string | null): Record<string, string> {
+    const headers: Record<string, string> = {
+      'Access-Control-Allow-Methods': 'POST, GET, OPTIONS',
+      'Access-Control-Allow-Headers': 'Content-Type, Authorization, Accept',
+    };
+    if (corsAllowlist && origin && corsAllowlist.has(origin)) {
+      headers['Access-Control-Allow-Origin'] = origin;
+      headers['Vary'] = 'Origin';
+    }
+    return headers;
+  }
+
+  async function validateToken(authHeader: string | null): Promise<AuthResult> {
+    if (!authHeader?.startsWith('Bearer ')) return { ok: false };
+    const token = authHeader.slice(7);
+    const hash = hashToken(token);
+    try {
+      const [row] = await sql`
+        SELECT id, name FROM access_tokens
+        WHERE token_hash = ${hash} AND revoked_at IS NULL
+      `;
+      if (!row) return { ok: false };
+      // Debounced last_used_at update — only writes once per token per 60s.
+      // SQL-level WHERE clause keeps this race-tolerant even under concurrent requests.
+      sql`UPDATE access_tokens
+          SET last_used_at = now()
+          WHERE id = ${row.id}
+            AND (last_used_at IS NULL OR last_used_at < now() - interval '60 seconds')`
+        .catch(() => { /* fire-and-forget */ });
+      return { ok: true, tokenId: row.id, tokenName: row.name };
+    } catch {
+      return { ok: false };
+    }
+  }
+
+  function logRequest(tokenName: string | null, operation: string, status: string, latencyMs: number) {
+    sql`INSERT INTO mcp_request_log (token_name, operation, latency_ms, status)
+        VALUES (${tokenName}, ${operation}, ${latencyMs}, ${status})`
+      .catch(() => { /* best-effort */ });
+  }
+
+  const server = Bun.serve({
+    port,
+    async fetch(req, server) {
+      const startedMs = Date.now();
+      const url = new URL(req.url);
+      const path = url.pathname;
+      const origin = req.headers.get('origin');
+
+      // CORS preflight
+      if (req.method === 'OPTIONS') {
+        return new Response(null, { headers: corsPreflightHeaders(origin) });
+      }
+
+      // Health check — no auth, no rate limit. Probes the DB so orchestration
+      // doesn't see "ok" while clients are getting misleading 401s during a DB outage.
+      if (path === '/health') {
+        try {
+          await sql`SELECT 1`;
+          return Response.json(
+            { status: 'ok', version: VERSION, transport: 'http', db: 'ok' },
+            { headers: corsHeaders(origin) },
+          );
+        } catch (e: any) {
+          return Response.json(
+            { status: 'unhealthy', version: VERSION, transport: 'http', db: 'unreachable', error: e?.message ?? 'unknown' },
+            { status: 503, headers: corsHeaders(origin) },
+          );
+        }
+      }
+
+      if (path !== '/mcp') {
+        return Response.json({ error: 'not_found' }, { status: 404, headers: corsHeaders(origin) });
+      }
+      if (req.method !== 'POST') {
+        return Response.json({ error: 'method_not_allowed' }, { status: 405, headers: corsHeaders(origin) });
+      }
+
+      const ip = resolveClientIp(req, server);
+
+      // Pre-auth IP rate limit. Fires BEFORE the DB lookup so we actually limit brute-force load.
+      const ipCheck = limiters.ip.check(ip);
+      if (!ipCheck.allowed) {
+        logRequest(null, 'unknown', 'rate_limited', Date.now() - startedMs);
+        return Response.json(
+          { error: 'rate_limited', message: 'Too many requests' },
+          {
+            status: 429,
+            headers: corsHeaders(origin, { 'Retry-After': String(ipCheck.retryAfter ?? 60) }),
+          },
+        );
+      }
+
+      // Body cap (stream-counted; chunked transfers caught here, not at req.json).
+      const bodyText = await readBodyWithCap(req, bodyCap);
+      if (bodyText === null) {
+        logRequest(null, 'unknown', 'body_too_large', Date.now() - startedMs);
+        return Response.json(
+          { error: 'payload_too_large', message: `Request body exceeds ${bodyCap} bytes` },
+          { status: 413, headers: corsHeaders(origin) },
+        );
+      }
+
+      // Auth.
+      const auth = await validateToken(req.headers.get('Authorization'));
+      if (!auth.ok) {
+        logRequest(null, 'unknown', 'auth_failed', Date.now() - startedMs);
+        return Response.json(
+          { error: 'invalid_token', message: 'Bearer token required. Create one: gbrain auth create <name>' },
+          { status: 401, headers: corsHeaders(origin) },
+        );
+      }
+
+      // Post-auth token-id rate limit. Limits runaway authed clients.
+      const tokCheck = limiters.token.check(auth.tokenId!);
+      if (!tokCheck.allowed) {
+        logRequest(auth.tokenName!, 'unknown', 'rate_limited', Date.now() - startedMs);
+        return Response.json(
+          { error: 'rate_limited', message: 'Too many requests for this token' },
+          {
+            status: 429,
+            headers: corsHeaders(origin, { 'Retry-After': String(tokCheck.retryAfter ?? 60) }),
+          },
+        );
+      }
+
+      // Parse JSON-RPC body.
+      let body: { method?: string; params?: any; id?: any };
+      try {
+        body = JSON.parse(bodyText);
+      } catch (e: any) {
+        logRequest(auth.tokenName!, 'unknown', 'parse_error', Date.now() - startedMs);
+        return Response.json(
+          { error: 'parse_error', message: e?.message ?? 'invalid JSON' },
+          { status: 400, headers: corsHeaders(origin) },
+        );
+      }
+
+      const { method, params, id } = body;
+
+      // initialize
+      if (method === 'initialize') {
+        logRequest(auth.tokenName!, 'initialize', 'success', Date.now() - startedMs);
+        return Response.json(
+          {
+            result: {
+              protocolVersion: '2025-03-26',
+              serverInfo: { name: 'gbrain', version: VERSION },
+              capabilities: { tools: {} },
+            },
+            jsonrpc: '2.0',
+            id,
+          },
+          { headers: corsHeaders(origin) },
+        );
+      }
+
+      // notifications/initialized — acknowledge with 204
+      if (method === 'notifications/initialized') {
+        return new Response(null, { status: 204, headers: corsHeaders(origin) });
+      }
+
+      // tools/list
+      if (method === 'tools/list') {
+        logRequest(auth.tokenName!, 'tools/list', 'success', Date.now() - startedMs);
+        return Response.json(
+          { result: { tools }, jsonrpc: '2.0', id },
+          { headers: corsHeaders(origin) },
+        );
+      }
+
+      // tools/call — dispatch through shared dispatch.ts (parity with stdio)
+      if (method === 'tools/call') {
+        const toolName: string = params?.name ?? 'unknown';
+        const args: Record<string, unknown> = params?.arguments ?? {};
+        const result = await dispatchToolCall(engine, toolName, args, { remote: true });
+        const status = result.isError ? 'error' : 'success';
+        logRequest(auth.tokenName!, `tools/call:${toolName}`, status, Date.now() - startedMs);
+        return Response.json(
+          { result, jsonrpc: '2.0', id },
+          { headers: corsHeaders(origin) },
+        );
+      }
+
+      logRequest(auth.tokenName!, method ?? 'unknown', 'unknown_method', Date.now() - startedMs);
+      return Response.json(
+        { error: 'unknown_method', message: `Unknown method: ${method}` },
+        { status: 400, headers: corsHeaders(origin) },
+      );
+    },
+  });
+
+  console.error(`GBrain HTTP MCP server running on port ${port}`);
+  console.error(`  Health: http://localhost:${port}/health`);
+  console.error(`  MCP:    http://localhost:${port}/mcp`);
+  console.error(`  Auth:   Bearer token required (create with: gbrain auth create <name>)`);
+  if (!corsAllowlist) {
+    console.error('  CORS:   default-deny. Set GBRAIN_HTTP_CORS_ORIGIN=https://your.app to allow browser clients.');
+  } else {
+    console.error(`  CORS:   allowlist = ${[...corsAllowlist].join(', ')}`);
+  }
+  console.error('');
+  console.error('⚠️  Do NOT use open OAuth registration for remote MCP access.');
+  console.error('   Tokens are managed via: gbrain auth create/list/revoke');
+
+  return server;
+}

src/mcp/rate-limit.ts

@@ -0,0 +1,142 @@
+/**
+ * Rate limiter for `gbrain serve --http`.
+ *
+ * Token-bucket per key, stored in a bounded LRU map so attacker-controlled keys
+ * can't grow memory unbounded. TTL prune on every access (entries older than
+ * 2× window are evicted) so abandoned keys don't sit around forever.
+ *
+ * Two buckets in the request pipeline (see http-transport.ts):
+ *   1. Pre-auth IP bucket — fires BEFORE the DB lookup so we actually limit
+ *      brute-force load against access_tokens, not just response codes.
+ *   2. Post-auth token-id bucket — fires after auth so legitimate-but-runaway
+ *      clients get throttled at the right principal.
+ *
+ * Both buckets behave identically; only the key differs.
+ */
+
+export interface RateLimitOpts {
+  /** Maximum requests in the window. */
+  limit: number;
+  /** Window length in milliseconds. */
+  windowMs: number;
+  /** LRU cap on distinct keys. Evicts least-recently-used on overflow. */
+  lruCap: number;
+}
+
+export interface RateLimitResult {
+  allowed: boolean;
+  /** Seconds until next request would be allowed (only set when !allowed). */
+  retryAfter?: number;
+  /** Tokens remaining in the bucket after this check. */
+  remaining: number;
+}
+
+interface Bucket {
+  tokens: number;
+  /** Used for refill math: tokens accrue based on elapsed time since this. */
+  lastRefillMs: number;
+  /** Used for TTL eviction: time of last check, regardless of refill. Prevents bucket-reset attack
+   *  where an exhausted key would otherwise get TTL-evicted and recreated fresh. */
+  lastTouchedMs: number;
+}
+
+/** Clock function — defaults to Date.now, overridable for tests. */
+type Clock = () => number;
+
+export class RateLimiter {
+  readonly opts: RateLimitOpts;
+  private readonly buckets: Map<string, Bucket> = new Map();
+  private readonly clock: Clock;
+
+  constructor(opts: RateLimitOpts, clock: Clock = Date.now) {
+    if (opts.limit <= 0) throw new Error('RateLimiter: limit must be > 0');
+    if (opts.windowMs <= 0) throw new Error('RateLimiter: windowMs must be > 0');
+    if (opts.lruCap <= 0) throw new Error('RateLimiter: lruCap must be > 0');
+    this.opts = opts;
+    this.clock = clock;
+  }
+
+  check(key: string): RateLimitResult {
+    const now = this.clock();
+    this.prune(now);
+
+    let bucket = this.buckets.get(key);
+    if (!bucket) {
+      bucket = { tokens: this.opts.limit, lastRefillMs: now, lastTouchedMs: now };
+    } else {
+      // Refill: tokens accrue continuously over the window. limit/windowMs tokens per ms.
+      const elapsed = now - bucket.lastRefillMs;
+      const refilled = Math.floor((elapsed * this.opts.limit) / this.opts.windowMs);
+      if (refilled > 0) {
+        bucket.tokens = Math.min(this.opts.limit, bucket.tokens + refilled);
+        bucket.lastRefillMs = now;
+      }
+      bucket.lastTouchedMs = now;
+      // LRU bookkeeping: re-insert to move to end (Map iteration order = insertion).
+      this.buckets.delete(key);
+    }
+
+    if (bucket.tokens > 0) {
+      bucket.tokens -= 1;
+      this.buckets.set(key, bucket);
+      this.evictIfOver();
+      return { allowed: true, remaining: bucket.tokens };
+    }
+
+    // No tokens. Compute Retry-After from when the next token will accrue.
+    const msPerToken = this.opts.windowMs / this.opts.limit;
+    const msUntilNext = msPerToken - (now - bucket.lastRefillMs);
+    const retryAfter = Math.max(1, Math.ceil(msUntilNext / 1000));
+    this.buckets.set(key, bucket);
+    this.evictIfOver();
+    return { allowed: false, retryAfter, remaining: 0 };
+  }
+
+  /** Evict TTL-expired entries (older than 2× window since last touch). Cheap: O(n) but n is bounded by lruCap.
+   *  Uses lastTouchedMs (not lastRefillMs) so an attacker can't reset their bucket by hammering an exhausted key
+   *  past the TTL — every check updates lastTouchedMs even when refill produces 0 tokens. */
+  private prune(now: number): void {
+    const ttl = this.opts.windowMs * 2;
+    for (const [key, bucket] of this.buckets) {
+      if (now - bucket.lastTouchedMs > ttl) {
+        this.buckets.delete(key);
+      } else {
+        // Map iteration is in insertion order; once we hit a fresh entry, the rest are also fresh
+        // ONLY if we maintain insertion-order = recency. That holds because check() does delete+set on every call.
+        break;
+      }
+    }
+  }
+
+  private evictIfOver(): void {
+    while (this.buckets.size > this.opts.lruCap) {
+      // Map iteration starts at oldest (first-inserted). Delete it.
+      const oldestKey = this.buckets.keys().next().value;
+      if (oldestKey === undefined) break;
+      this.buckets.delete(oldestKey);
+    }
+  }
+
+  /** Test helper: current key count. */
+  get size(): number {
+    return this.buckets.size;
+  }
+}
+
+/** Parse a positive integer env var, falling back to default. */
+function envInt(name: string, fallback: number): number {
+  const v = process.env[name];
+  if (!v) return fallback;
+  const n = parseInt(v, 10);
+  return Number.isFinite(n) && n > 0 ? n : fallback;
+}
+
+/** Build limiters from env. Keep this lazy — tests can construct RateLimiter directly. */
+export function buildDefaultLimiters(clock: Clock = Date.now): { ip: RateLimiter; token: RateLimiter } {
+  const lruCap = envInt('GBRAIN_HTTP_RATE_LIMIT_LRU', 10000);
+  const windowMs = 60_000;
+  return {
+    ip: new RateLimiter({ limit: envInt('GBRAIN_HTTP_RATE_LIMIT_IP', 30), windowMs, lruCap }, clock),
+    token: new RateLimiter({ limit: envInt('GBRAIN_HTTP_RATE_LIMIT_TOKEN', 60), windowMs, lruCap }, clock),
+  };
+}

src/mcp/server.ts

@@ -2,30 +2,10 @@ import { Server } from '@modelcontextprotocol/sdk/server/index.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 import { ListToolsRequestSchema, CallToolRequestSchema } from '@modelcontextprotocol/sdk/types.js';
 import type { BrainEngine } from '../core/engine.ts';
-import { operations, OperationError } from '../core/operations.ts';
-import type { Operation, OperationContext } from '../core/operations.ts';
-import { loadConfig } from '../core/config.ts';
+import { operations } from '../core/operations.ts';
 import { VERSION } from '../version.ts';
 import { buildToolDefs } from './tool-defs.ts';
-
-/** Validate required params exist and have the expected type */
-function validateParams(op: Operation, params: Record<string, unknown>): string | null {
-  for (const [key, def] of Object.entries(op.params)) {
-    if (def.required && (params[key] === undefined || params[key] === null)) {
-      return `Missing required parameter: ${key}`;
-    }
-    if (params[key] !== undefined && params[key] !== null) {
-      const val = params[key];
-      const expected = def.type;
-      if (expected === 'string' && typeof val !== 'string') return `Parameter "${key}" must be a string`;
-      if (expected === 'number' && typeof val !== 'number') return `Parameter "${key}" must be a number`;
-      if (expected === 'boolean' && typeof val !== 'boolean') return `Parameter "${key}" must be a boolean`;
-      if (expected === 'object' && (typeof val !== 'object' || Array.isArray(val))) return `Parameter "${key}" must be an object`;
-      if (expected === 'array' && !Array.isArray(val)) return `Parameter "${key}" must be an array`;
-    }
-  }
-  return null;
-}
+import { dispatchToolCall, validateParams, buildOperationContext } from './dispatch.ts';
 
 export async function startMcpServer(engine: BrainEngine) {
   const server = new Server(
@@ -40,50 +20,21 @@ export async function startMcpServer(engine: BrainEngine) {
     tools: buildToolDefs(operations),
   }));
 
-  // Dispatch tool calls to operation handlers
-  server.setRequestHandler(CallToolRequestSchema, async (request: any) => {
+  // Dispatch tool calls via shared dispatch.ts (parity with HTTP transport).
+  // MCP stdio callers are remote/untrusted; dispatch defaults remote=true.
+  // The MCP SDK's response type widened in 1.29 to allow a managed-task wrapper;
+  // gbrain ops are synchronous, so we return the legacy `{ content, isError? }`
+  // shape and cast through `any` (the SDK accepts it via the ServerResult union).
+  server.setRequestHandler(CallToolRequestSchema, async (request: any): Promise<any> => {
     const { name, arguments: params } = request.params;
-    const op = operations.find(o => o.name === name);
-    if (!op) {
-      return { content: [{ type: 'text', text: `Error: Unknown tool: ${name}` }], isError: true };
-    }
-
-    const ctx: OperationContext = {
-      engine,
-      config: loadConfig() || { engine: 'postgres' },
-      logger: {
-        info: (msg: string) => process.stderr.write(`[info] ${msg}\n`),
-        warn: (msg: string) => process.stderr.write(`[warn] ${msg}\n`),
-        error: (msg: string) => process.stderr.write(`[error] ${msg}\n`),
-      },
-      dryRun: !!(params?.dry_run),
-      // MCP stdio callers are remote/untrusted; enforce strict file confinement.
-      remote: true,
-    };
-
-    const safeParams = params || {};
-    const validationError = validateParams(op, safeParams);
-    if (validationError) {
-      return { content: [{ type: 'text', text: JSON.stringify({ error: 'invalid_params', message: validationError }, null, 2) }], isError: true };
-    }
-
-    try {
-      const result = await op.handler(ctx, safeParams);
-      return { content: [{ type: 'text', text: JSON.stringify(result, null, 2) }] };
-    } catch (e: unknown) {
-      if (e instanceof OperationError) {
-        return { content: [{ type: 'text', text: JSON.stringify(e.toJSON(), null, 2) }], isError: true };
-      }
-      const msg = e instanceof Error ? e.message : String(e);
-      return { content: [{ type: 'text', text: `Error: ${msg}` }], isError: true };
-    }
+    return dispatchToolCall(engine, name, params, { remote: true });
   });
 
   const transport = new StdioServerTransport();
   await server.connect(transport);
 }
 
-// Backward compat: used by `gbrain call` command
+// Backward compat: used by `gbrain call` command (trusted local path).
 export async function handleToolCall(
   engine: BrainEngine,
   tool: string,
@@ -95,14 +46,10 @@ export async function handleToolCall(
   const validationError = validateParams(op, params);
   if (validationError) throw new Error(validationError);
 
-  const ctx: OperationContext = {
-    engine,
-    config: loadConfig() || { engine: 'postgres' },
-    logger: { info: console.log, warn: console.warn, error: console.error },
-    dryRun: !!(params?.dry_run),
-    // Backing path for `gbrain call` CLI command — trusted local invocation.
+  const ctx = buildOperationContext(engine, params, {
     remote: false,
-  };
+    logger: { info: console.log, warn: console.warn, error: console.error },
+  });
 
   return op.handler(ctx, params);
 }

test/bootstrap.test.ts

@@ -0,0 +1,192 @@
+/**
+ * PGLite forward-reference bootstrap tests.
+ *
+ * Validates the contract of `PGLiteEngine#applyForwardReferenceBootstrap`:
+ * given a brain that lacks the schema-blob's forward-referenced state, the
+ * bootstrap adds enough state for PGLITE_SCHEMA_SQL to replay safely.
+ *
+ * The bootstrap covers the wedge incidents from issues
+ * #239/#266/#357/#366/#374/#375/#378/#396 — every gbrain release that added
+ * a column-with-index in the schema blob without a corresponding bootstrap
+ * triggered the same wedge family.
+ *
+ * Honest limitation: test 4 simulates a v20 brain by dropping known forward
+ * state from a fresh-LATEST instance. This is the same down-mutation pattern
+ * codex flagged as "weak simulation" — it can't simulate every possible
+ * historical state. Acceptable here because the bootstrap's contract is
+ * narrow ("given a brain that lacks the specific forward-references,
+ * initSchema produces a brain at LATEST"), and that contract is exactly
+ * what this test exercises.
+ */
+
+import { describe, test, expect } from 'bun:test';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { LATEST_VERSION } from '../src/core/migrate.ts';
+
+describe('PGLiteEngine#applyForwardReferenceBootstrap', () => {
+  test('no-op on fresh install (no pages or links table)', async () => {
+    const engine = new PGLiteEngine();
+    await engine.connect({});
+    try {
+      // Don't call initSchema — verify bootstrap alone does nothing on empty DB
+      await (engine as any).applyForwardReferenceBootstrap();
+      const { rows } = await (engine as any).db.query(`
+        SELECT COUNT(*)::int AS c FROM information_schema.tables
+        WHERE table_schema = 'public'
+      `);
+      expect(rows[0].c).toBe(0);
+    } finally {
+      await engine.disconnect();
+    }
+  }, 30000);
+
+  test('idempotent: calling twice produces same result', async () => {
+    const engine = new PGLiteEngine();
+    await engine.connect({});
+    try {
+      await engine.initSchema();
+      const db = (engine as any).db;
+
+      // Mutate to pre-v0.18 shape: drop source_id and the sources FK target
+      await db.exec(`
+        ALTER TABLE pages DROP CONSTRAINT IF EXISTS pages_source_slug_key;
+        ALTER TABLE pages ADD CONSTRAINT pages_slug_key UNIQUE (slug);
+        DROP INDEX IF EXISTS idx_pages_source_id;
+        ALTER TABLE pages DROP COLUMN IF EXISTS source_id;
+        DROP TABLE IF EXISTS sources CASCADE;
+      `);
+
+      // First call: applies bootstrap
+      await (engine as any).applyForwardReferenceBootstrap();
+      // Second call: must not error, must not duplicate state
+      await (engine as any).applyForwardReferenceBootstrap();
+
+      const { rows: cols } = await db.query(`
+        SELECT column_name FROM information_schema.columns
+        WHERE table_name = 'pages' AND column_name = 'source_id'
+      `);
+      expect(cols).toHaveLength(1);
+
+      const { rows: src } = await db.query(`SELECT COUNT(*)::int AS c FROM sources`);
+      expect(src[0].c).toBe(1); // 'default' seed not duplicated
+    } finally {
+      await engine.disconnect();
+    }
+  }, 30000);
+
+  test('no-op on modern brain (source_id and links provenance already present)', async () => {
+    const engine = new PGLiteEngine();
+    await engine.connect({});
+    try {
+      await engine.initSchema();
+      const db = (engine as any).db;
+
+      const before = await db.query(`SELECT COUNT(*)::int AS c FROM sources`);
+      await (engine as any).applyForwardReferenceBootstrap();
+      const after = await db.query(`SELECT COUNT(*)::int AS c FROM sources`);
+
+      // Bootstrap probe should detect the brain is modern and skip the seed insert
+      expect(after.rows[0].c).toBe(before.rows[0].c);
+    } finally {
+      await engine.disconnect();
+    }
+  }, 30000);
+
+  test('full path: pre-v0.18 brain reaches LATEST_VERSION via initSchema', async () => {
+    const engine = new PGLiteEngine();
+    await engine.connect({});
+    try {
+      await engine.initSchema();
+      const db = (engine as any).db;
+
+      // Mutate to pre-v0.18 shape: strip the forward-referenced state.
+      // Match the shape from #399's regression fixture; constraints first
+      // (so dropping columns succeeds).
+      await db.exec(`
+        ALTER TABLE pages DROP CONSTRAINT IF EXISTS pages_source_slug_key;
+        ALTER TABLE pages ADD CONSTRAINT pages_slug_key UNIQUE (slug);
+        DROP INDEX IF EXISTS idx_pages_source_id;
+        ALTER TABLE pages DROP COLUMN IF EXISTS source_id;
+        DROP TABLE IF EXISTS sources CASCADE;
+        ALTER TABLE links DROP CONSTRAINT IF EXISTS links_resolution_type_check;
+        ALTER TABLE links DROP COLUMN IF EXISTS resolution_type;
+      `);
+      await engine.setConfig('version', '20');
+
+      // Path under test: bootstrap → SCHEMA_SQL → runMigrations
+      await engine.initSchema();
+
+      expect(await engine.getConfig('version')).toBe(String(LATEST_VERSION));
+
+      const { rows: srcCol } = await db.query(`
+        SELECT column_name FROM information_schema.columns
+        WHERE table_name = 'pages' AND column_name = 'source_id'
+      `);
+      expect(srcCol).toHaveLength(1);
+
+      const { rows: defaultSrc } = await db.query(`SELECT id FROM sources WHERE id = 'default'`);
+      expect(defaultSrc).toHaveLength(1);
+    } finally {
+      await engine.disconnect();
+    }
+  }, 30000);
+
+  test('fresh install regression: initSchema on empty DB produces LATEST', async () => {
+    // The bootstrap's table-existence probe must not mis-classify "no table"
+    // as "pre-v0.18 brain." Without the table-existence guard, the bootstrap
+    // would call runMigrations against an empty DB and crash on
+    // `relation "config" does not exist`. Regression test for that path.
+    const engine = new PGLiteEngine();
+    await engine.connect({});
+    try {
+      await engine.initSchema();
+      expect(await engine.getConfig('version')).toBe(String(LATEST_VERSION));
+
+      const db = (engine as any).db;
+      const pages = await db.query(`SELECT 1 FROM pages LIMIT 0`);
+      const sources = await db.query(`SELECT 1 FROM sources LIMIT 0`);
+      const config = await db.query(`SELECT 1 FROM config LIMIT 0`);
+      expect(pages).toBeDefined();
+      expect(sources).toBeDefined();
+      expect(config).toBeDefined();
+    } finally {
+      await engine.disconnect();
+    }
+  }, 30000);
+
+  test('pre-v0.13 links shape: bootstrap adds link_source + origin_page_id', async () => {
+    // Issues #266 / #357 — pre-v0.13 brains had `links` without
+    // `link_source` / `origin_page_id`. Schema blob's
+    // `CREATE INDEX idx_links_source` would crash before v11 ran.
+    const engine = new PGLiteEngine();
+    await engine.connect({});
+    try {
+      await engine.initSchema();
+      const db = (engine as any).db;
+
+      await db.exec(`
+        DROP INDEX IF EXISTS idx_links_source;
+        DROP INDEX IF EXISTS idx_links_origin;
+        ALTER TABLE links DROP CONSTRAINT IF EXISTS links_from_to_type_source_origin_unique;
+        ALTER TABLE links DROP COLUMN IF EXISTS link_source;
+        ALTER TABLE links DROP COLUMN IF EXISTS origin_page_id;
+      `);
+
+      await (engine as any).applyForwardReferenceBootstrap();
+
+      const { rows: lsCol } = await db.query(`
+        SELECT column_name FROM information_schema.columns
+        WHERE table_name = 'links' AND column_name = 'link_source'
+      `);
+      expect(lsCol).toHaveLength(1);
+
+      const { rows: opCol } = await db.query(`
+        SELECT column_name FROM information_schema.columns
+        WHERE table_name = 'links' AND column_name = 'origin_page_id'
+      `);
+      expect(opCol).toHaveLength(1);
+    } finally {
+      await engine.disconnect();
+    }
+  }, 30000);
+});

test/brain-writer.test.ts

@@ -1,4 +1,4 @@
-import { describe, expect, test, beforeEach, afterEach } from 'bun:test';
+import { describe, expect, test, beforeAll, afterAll, beforeEach, afterEach } from 'bun:test';
 import { mkdtempSync, rmSync, writeFileSync, readFileSync, existsSync, mkdirSync, symlinkSync } from 'fs';
 import { join } from 'path';
 import { tmpdir } from 'os';
@@ -9,6 +9,7 @@ import {
   BrainWriterError,
 } from '../src/core/brain-writer.ts';
 import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { resetPgliteState } from './helpers/reset-pglite.ts';
 
 const fence = '---';
 
@@ -115,15 +116,24 @@ describe('scanBrainSources (PGLite)', () => {
   let tmp: string;
   let engine: PGLiteEngine;
 
-  beforeEach(async () => {
-    tmp = mkdtempSync(join(tmpdir(), 'brain-writer-scan-'));
+  // One PGLite per file — beforeEach wipes data only. PGLite cold-start is
+  // ~20s on CI; sharing one engine across 6 tests in this block saves ~2 min.
+  beforeAll(async () => {
     engine = new PGLiteEngine();
     await engine.connect({});
     await engine.initSchema();
   });
 
-  afterEach(async () => {
+  afterAll(async () => {
     await engine.disconnect();
+  });
+
+  beforeEach(async () => {
+    await resetPgliteState(engine);
+    tmp = mkdtempSync(join(tmpdir(), 'brain-writer-scan-'));
+  });
+
+  afterEach(() => {
     rmSync(tmp, { recursive: true, force: true });
   });
 

test/cycle-abort.test.ts

@@ -108,7 +108,7 @@ describe('autopilot-cycle handler contract (v0.20.5)', () => {
     // This is a source-level regression guard
     const handlerBlock = jobsSource.slice(
       jobsSource.indexOf("worker.register('autopilot-cycle'"),
-      jobsSource.indexOf("worker.register('autopilot-cycle'") + 500,
+      jobsSource.indexOf("worker.register('autopilot-cycle'") + 2000,
     );
 
     expect(handlerBlock).toContain('signal: job.signal');

test/disk-walk.test.ts

@@ -0,0 +1,92 @@
+/**
+ * Tests for src/core/disk-walk.ts — single-walk filesystem scan.
+ *
+ * Replaces the per-page existsSync+statSync syscall storm in storage.ts
+ * (Issue #14 of the v0.22.3 eng review).
+ */
+
+import { describe, test, expect, beforeEach, afterEach } from 'bun:test';
+import { mkdtempSync, mkdirSync, rmSync, writeFileSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { walkBrainRepo } from '../src/core/disk-walk.ts';
+
+let tmp: string;
+
+beforeEach(() => {
+  tmp = mkdtempSync(join(tmpdir(), 'gbrain-walk-test-'));
+});
+
+afterEach(() => {
+  rmSync(tmp, { recursive: true, force: true });
+});
+
+function write(relPath: string, content: string): void {
+  const full = join(tmp, relPath);
+  mkdirSync(join(full, '..'), { recursive: true });
+  writeFileSync(full, content);
+}
+
+describe('walkBrainRepo', () => {
+  test('returns empty map for empty directory', () => {
+    expect(walkBrainRepo(tmp).size).toBe(0);
+  });
+
+  test('returns empty map for nonexistent directory', () => {
+    expect(walkBrainRepo(join(tmp, 'does-not-exist')).size).toBe(0);
+  });
+
+  test('finds top-level .md files keyed by slug (no .md suffix)', () => {
+    write('alice.md', '# Alice');
+    const result = walkBrainRepo(tmp);
+    expect(result.has('alice')).toBe(true);
+    expect(result.get('alice')!.size).toBeGreaterThan(0);
+  });
+
+  test('walks nested directories and produces slash-joined slugs', () => {
+    write('people/alice.md', '# Alice');
+    write('media/x/tweet-1.md', 'tweet');
+    write('media/articles/post-1.md', 'post');
+    const result = walkBrainRepo(tmp);
+    expect(new Set(result.keys())).toEqual(
+      new Set(['people/alice', 'media/x/tweet-1', 'media/articles/post-1']),
+    );
+  });
+
+  test('skips dot-directories (.git, .gbrain, .vscode)', () => {
+    write('.git/HEAD', 'ref: refs/heads/main');
+    write('.gbrain/config.json', '{}');
+    write('.vscode/settings.json', '{}');
+    write('people/alice.md', '# Alice');
+    const result = walkBrainRepo(tmp);
+    expect(new Set(result.keys())).toEqual(new Set(['people/alice']));
+  });
+
+  test('skips node_modules', () => {
+    write('node_modules/foo/bar.md', 'noise');
+    write('people/alice.md', '# Alice');
+    const result = walkBrainRepo(tmp);
+    expect(new Set(result.keys())).toEqual(new Set(['people/alice']));
+  });
+
+  test('ignores non-.md files', () => {
+    write('people/alice.md', '# Alice');
+    write('people/alice.json', '{}');
+    write('people/photo.png', 'binary');
+    const result = walkBrainRepo(tmp);
+    expect(new Set(result.keys())).toEqual(new Set(['people/alice']));
+  });
+
+  test('captures size from stat', () => {
+    const content = '# Alice\n'.repeat(100);
+    write('people/alice.md', content);
+    const result = walkBrainRepo(tmp);
+    expect(result.get('people/alice')!.size).toBe(content.length);
+  });
+
+  test('captures mtimeMs', () => {
+    write('people/alice.md', '# Alice');
+    const result = walkBrainRepo(tmp);
+    expect(result.get('people/alice')!.mtimeMs).toBeGreaterThan(0);
+  });
+});

test/e2e/http-transport.test.ts

@@ -0,0 +1,233 @@
+/**
+ * E2E tests for src/mcp/http-transport.ts against real Postgres.
+ *
+ * Catches schema drift (column-name typos that would slip past the unit suite's
+ * stubbed engine.sql) and proves the F1+F2+F3 dispatch pipeline works against a
+ * real handler doing real DB work. Also exercises the SQL-level last_used_at
+ * debounce against real Postgres semantics.
+ *
+ * Run: DATABASE_URL=... bun test test/e2e/http-transport.test.ts
+ */
+
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import { createHash, randomBytes } from 'crypto';
+import { startHttpTransport } from '../../src/mcp/http-transport.ts';
+import { hasDatabase, setupDB, teardownDB, getEngine, getConn } from './helpers.ts';
+
+const skip = !hasDatabase();
+const describeE2E = skip ? describe.skip : describe;
+
+if (skip) {
+  console.log('Skipping E2E http-transport tests (DATABASE_URL not set)');
+}
+
+interface ServerHandle {
+  port: number;
+  stop: () => Promise<void>;
+}
+
+function generateToken(): string {
+  return 'gbrain_test_' + randomBytes(16).toString('hex');
+}
+
+function hashToken(token: string): string {
+  return createHash('sha256').update(token).digest('hex');
+}
+
+async function startServer(): Promise<ServerHandle> {
+  const engine = getEngine();
+  const server = await startHttpTransport({ port: 0, engine: engine as any });
+  return {
+    port: (server as any).port,
+    stop: async () => { (server as any).stop(true); },
+  };
+}
+
+function rpc(method: string, params?: unknown, id: number = 1) {
+  return JSON.stringify({ jsonrpc: '2.0', id, method, ...(params !== undefined ? { params } : {}) });
+}
+
+describeE2E('http-transport E2E (real Postgres)', () => {
+  let srv: ServerHandle;
+  let validToken: string;
+  let revokedToken: string;
+  let validTokenName: string;
+
+  beforeAll(async () => {
+    await setupDB();
+    const conn = getConn();
+
+    // Seed a valid + revoked token directly via SQL (mirrors auth.ts's create path).
+    validToken = generateToken();
+    validTokenName = 'e2e-valid-' + randomBytes(4).toString('hex');
+    await conn.unsafe(
+      'INSERT INTO access_tokens (name, token_hash) VALUES ($1, $2)',
+      [validTokenName, hashToken(validToken)],
+    );
+    revokedToken = generateToken();
+    await conn.unsafe(
+      'INSERT INTO access_tokens (name, token_hash, revoked_at) VALUES ($1, $2, now())',
+      ['e2e-revoked-' + randomBytes(4).toString('hex'), hashToken(revokedToken)],
+    );
+
+    srv = await startServer();
+  });
+
+  afterAll(async () => {
+    if (srv) await srv.stop();
+    await teardownDB();
+  });
+
+  test('1. /health → 200 with expected JSON shape', async () => {
+    const r = await fetch(`http://localhost:${srv.port}/health`);
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.status).toBe('ok');
+    expect(body.transport).toBe('http');
+    expect(body.version).toBeString();
+  });
+
+  test('2. /mcp tools/list with valid Bearer → 200 + ops list', async () => {
+    const r = await fetch(`http://localhost:${srv.port}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${validToken}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.result.tools).toBeArray();
+    expect(body.result.tools.length).toBeGreaterThan(5);
+    expect(r.headers.get('content-type')).toContain('application/json');
+  });
+
+  test('3. /mcp tools/call (real op: list_pages) round-trips successfully — F1+F2+F3 guard', async () => {
+    const r = await fetch(`http://localhost:${srv.port}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${validToken}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/call', { name: 'list_pages', arguments: { limit: 5 } }),
+    });
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.jsonrpc).toBe('2.0');
+    expect(body.result.content).toBeArray();
+    // Should NOT be an error — handler ran successfully against the real engine.
+    expect(body.result.isError).toBeUndefined();
+    // Result text should parse as JSON (list_pages returns an object/array)
+    const resultText = body.result.content[0].text;
+    const parsed = JSON.parse(resultText);
+    expect(parsed).toBeDefined();
+  });
+
+  test('4. revoked token → 401', async () => {
+    const r = await fetch(`http://localhost:${srv.port}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${revokedToken}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    expect(r.status).toBe(401);
+  });
+
+  test('5. last_used_at debounce: two consecutive valid calls → only one UPDATE within 60s', async () => {
+    const conn = getConn();
+
+    // Reset last_used_at to NULL so the first call definitely updates
+    await conn.unsafe('UPDATE access_tokens SET last_used_at = NULL WHERE name = $1', [validTokenName]);
+
+    // First request — should update last_used_at
+    await fetch(`http://localhost:${srv.port}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${validToken}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    // Give the fire-and-forget UPDATE a moment to land
+    await new Promise(r => setTimeout(r, 50));
+
+    const [row1] = await conn.unsafe(
+      'SELECT last_used_at FROM access_tokens WHERE name = $1',
+      [validTokenName],
+    ) as { last_used_at: Date | null }[];
+    expect(row1.last_used_at).not.toBeNull();
+    const firstUpdate = row1.last_used_at;
+
+    // Second request immediately — should NOT trigger another UPDATE (debounced by SQL WHERE)
+    await fetch(`http://localhost:${srv.port}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${validToken}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    await new Promise(r => setTimeout(r, 50));
+
+    const [row2] = await conn.unsafe(
+      'SELECT last_used_at FROM access_tokens WHERE name = $1',
+      [validTokenName],
+    ) as { last_used_at: Date | null }[];
+    // Same timestamp = same UPDATE = debounce held
+    expect(row2.last_used_at?.getTime()).toBe(firstUpdate?.getTime());
+  });
+
+  test('6. last_used_at debounce: simulating 65s gap → second request DOES update', async () => {
+    const conn = getConn();
+
+    // Set last_used_at to 65 seconds ago — simulates the time gap without waiting in real time
+    await conn.unsafe(
+      `UPDATE access_tokens SET last_used_at = now() - interval '65 seconds' WHERE name = $1`,
+      [validTokenName],
+    );
+    const [before] = await conn.unsafe(
+      'SELECT last_used_at FROM access_tokens WHERE name = $1',
+      [validTokenName],
+    ) as { last_used_at: Date | null }[];
+
+    await fetch(`http://localhost:${srv.port}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${validToken}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    await new Promise(r => setTimeout(r, 50));
+
+    const [after] = await conn.unsafe(
+      'SELECT last_used_at FROM access_tokens WHERE name = $1',
+      [validTokenName],
+    ) as { last_used_at: Date | null }[];
+    expect(after.last_used_at?.getTime()).toBeGreaterThan(before.last_used_at!.getTime());
+  });
+
+  test('7. mcp_request_log gets a row per request', async () => {
+    const conn = getConn();
+    const beforeRows = await conn.unsafe('SELECT count(*)::int AS n FROM mcp_request_log') as { n: number }[];
+    const beforeN = beforeRows[0].n;
+
+    await fetch(`http://localhost:${srv.port}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${validToken}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    // Fire-and-forget audit insert — give it a tick
+    await new Promise(r => setTimeout(r, 100));
+
+    const afterRows = await conn.unsafe('SELECT count(*)::int AS n FROM mcp_request_log') as { n: number }[];
+    expect(afterRows[0].n).toBeGreaterThan(beforeN);
+
+    const [row] = await conn.unsafe(
+      `SELECT token_name, operation, status, latency_ms FROM mcp_request_log
+       WHERE token_name = $1 ORDER BY created_at DESC LIMIT 1`,
+      [validTokenName],
+    ) as { token_name: string; operation: string; status: string; latency_ms: number }[];
+    expect(row.token_name).toBe(validTokenName);
+    expect(row.operation).toBe('tools/list');
+    expect(row.status).toBe('success');
+    expect(row.latency_ms).toBeGreaterThanOrEqual(0);
+  });
+
+  test('8. tools/call with malformed params → isError result with invalid_params', async () => {
+    const r = await fetch(`http://localhost:${srv.port}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${validToken}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/call', { name: 'get_page', arguments: { slug: 42 } }),
+    });
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.result.isError).toBe(true);
+    expect(body.result.content[0].text).toContain('invalid_params');
+  });
+});

test/e2e/integrity-batch.test.ts

@@ -0,0 +1,168 @@
+/**
+ * E2E parity tests — scanIntegrity batch path vs sequential path.
+ *
+ * The batch path (Postgres-only fast path added in v0.20.x) and the sequential
+ * path (engine.getAllSlugs + getPage loop) MUST return the same result for
+ * every supported case, otherwise gbrain doctor reports different numbers
+ * depending on engine type or whether batch was attempted.
+ *
+ * Codex review of the original perf commit caught a multi-source dedup
+ * regression: the batch SQL scanned raw (source_id, slug) rows while
+ * sequential's getAllSlugs() returned a Set<string>. v0.22.7 adds
+ * SELECT DISTINCT ON (slug) to the batch SQL; these tests prove parity.
+ *
+ * Run: DATABASE_URL=... bun test test/e2e/integrity-batch.test.ts
+ */
+
+import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
+import { hasDatabase, setupDB, teardownDB, getEngine, getConn } from './helpers.ts';
+import { scanIntegrity } from '../../src/commands/integrity.ts';
+
+const skip = !hasDatabase();
+const describeE2E = skip ? describe.skip : describe;
+
+if (skip) {
+  console.log('Skipping E2E integrity batch parity tests (DATABASE_URL not set)');
+}
+
+describeE2E('scanIntegrity batch parity (E2E, Postgres-only)', () => {
+  beforeAll(async () => {
+    await setupDB();
+  });
+
+  afterAll(async () => {
+    await teardownDB();
+  });
+
+  beforeEach(async () => {
+    // Clean slate per case so fixtures don't leak across describes.
+    const conn = getConn();
+    await conn.unsafe(`TRUNCATE pages CASCADE`);
+  });
+
+  describe('dedup', () => {
+    test('multi-source duplicate slugs scan once, not once-per-source', async () => {
+      const engine = getEngine();
+      const conn = getConn();
+
+      // Seed default-source page via the engine.
+      await engine.putPage('people/alice', {
+        type: 'person',
+        title: 'Alice',
+        compiled_truth: 'Alice writes about AI safety.',
+        timeline: '',
+        frontmatter: {},
+      });
+
+      // Seed alt-source row via raw SQL — engine.putPage doesn't take a source_id,
+      // and we specifically need to test that DISTINCT ON (slug) collapses
+      // the multi-source rows into one scan.
+      await conn.unsafe(`
+        INSERT INTO sources (id, name) VALUES ('test-source-2', 'test-source-2')
+        ON CONFLICT DO NOTHING
+      `);
+      await conn.unsafe(`
+        INSERT INTO pages (source_id, slug, type, title, compiled_truth, timeline, frontmatter)
+        VALUES ('test-source-2', 'people/alice', 'person', 'Alice (alt source)',
+                'Alice from another source.', '', '{}'::jsonb)
+      `);
+
+      const batchResult = await scanIntegrity(engine, { limit: 100, batchLoad: true });
+      const seqResult = await scanIntegrity(engine, { limit: 100, batchLoad: false });
+
+      // Both paths must report the same number of distinct slugs scanned.
+      // Pre-fix: batch reported 2 (one per source row), sequential reported 1.
+      expect(batchResult.pagesScanned).toBe(seqResult.pagesScanned);
+      expect(batchResult.pagesScanned).toBe(1);
+    });
+  });
+
+  describe('hits', () => {
+    test('bareHits and externalHits arrays match between paths', async () => {
+      const engine = getEngine();
+
+      await engine.putPage('people/alice', {
+        type: 'person',
+        title: 'Alice',
+        compiled_truth: 'Alice tweeted about AI safety last week.',
+        timeline: '',
+        frontmatter: {},
+      });
+      await engine.putPage('people/bob', {
+        type: 'person',
+        title: 'Bob',
+        compiled_truth: 'Bob wrote at [example](https://example.com/bob).',
+        timeline: '',
+        frontmatter: {},
+      });
+
+      const batchResult = await scanIntegrity(engine, { limit: 100, batchLoad: true });
+      const seqResult = await scanIntegrity(engine, { limit: 100, batchLoad: false });
+
+      expect(batchResult.bareHits.length).toBe(seqResult.bareHits.length);
+      expect(batchResult.externalHits.length).toBe(seqResult.externalHits.length);
+      expect(batchResult.bareHits.map(h => h.slug).sort()).toEqual(
+        seqResult.bareHits.map(h => h.slug).sort(),
+      );
+      expect(batchResult.externalHits.map(h => h.slug).sort()).toEqual(
+        seqResult.externalHits.map(h => h.slug).sort(),
+      );
+    });
+  });
+
+  describe('validate', () => {
+    test('validate:false (boolean) page is skipped on both paths', async () => {
+      const engine = getEngine();
+
+      await engine.putPage('people/alice', {
+        type: 'person',
+        title: 'Alice',
+        compiled_truth: 'Alice tweeted about something.',
+        timeline: '',
+        frontmatter: {},
+      });
+      await engine.putPage('people/legacy', {
+        type: 'person',
+        title: 'Legacy',
+        compiled_truth: 'Legacy tweeted about old stuff.',
+        timeline: '',
+        frontmatter: { validate: false },
+      });
+
+      const batchResult = await scanIntegrity(engine, { limit: 100, batchLoad: true });
+      const seqResult = await scanIntegrity(engine, { limit: 100, batchLoad: false });
+
+      expect(batchResult.pagesScanned).toBe(seqResult.pagesScanned);
+      expect(batchResult.pagesScanned).toBe(1);
+      expect(batchResult.bareHits.map(h => h.slug)).not.toContain('people/legacy');
+      expect(seqResult.bareHits.map(h => h.slug)).not.toContain('people/legacy');
+    });
+  });
+
+  describe('topPages', () => {
+    test('topPages ordering matches between paths', async () => {
+      const engine = getEngine();
+
+      // Alice has 2 bare-tweet hits; Bob has 1.
+      await engine.putPage('people/alice', {
+        type: 'person',
+        title: 'Alice',
+        compiled_truth: 'Alice tweeted today. Alice tweeted yesterday too.',
+        timeline: '',
+        frontmatter: {},
+      });
+      await engine.putPage('people/bob', {
+        type: 'person',
+        title: 'Bob',
+        compiled_truth: 'Bob tweeted once.',
+        timeline: '',
+        frontmatter: {},
+      });
+
+      const batchResult = await scanIntegrity(engine, { limit: 100, batchLoad: true });
+      const seqResult = await scanIntegrity(engine, { limit: 100, batchLoad: false });
+
+      expect(batchResult.topPages).toEqual(seqResult.topPages);
+    });
+  });
+});

test/e2e/minions-shell-pglite.test.ts

@@ -43,7 +43,7 @@ beforeAll(async () => {
   engine = new PGLiteEngine();
   await engine.connect({}); // in-memory PGLite
   await engine.initSchema(); // installs pages, minion_jobs, config, etc.
-});
+}, 30000);
 
 afterAll(async () => {
   await engine.disconnect();

test/e2e/postgres-bootstrap.test.ts

@@ -0,0 +1,93 @@
+/**
+ * E2E test for PostgresEngine forward-reference bootstrap.
+ *
+ * Codex caught that `test/e2e/helpers.ts:74` uses the standalone
+ * `db.initSchema()` from `src/core/db.ts`, which only runs SCHEMA_SQL and
+ * never calls runMigrations(). A test using that helper would NOT exercise
+ * `PostgresEngine.initSchema()`'s reordered path, producing false-positive
+ * coverage. This test deliberately bypasses the standard helper and
+ * instantiates `PostgresEngine` directly, calling `engine.initSchema()` so
+ * the bootstrap → SCHEMA_SQL → runMigrations sequence runs end-to-end.
+ *
+ * Covers issues #366, #375, #378 — Postgres-side wedges where pre-v0.18
+ * brains crashed on `column "source_id" does not exist`.
+ *
+ * NOTE: snapshot-based historical state simulation is out of scope for this
+ * wave (would require maintaining historical schema dumps). The test
+ * mutates a fresh-LATEST brain to a pre-v0.18 shape; codex flagged this as
+ * approximate. Acceptable here because the bootstrap's contract is narrow:
+ * "given a brain that lacks the specific forward-references, initSchema
+ * produces a brain at LATEST." The test exercises exactly that contract.
+ *
+ * Run: DATABASE_URL=postgresql://... bun run test:e2e test/e2e/postgres-bootstrap.test.ts
+ */
+
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import { PostgresEngine } from '../../src/core/postgres-engine.ts';
+import { LATEST_VERSION } from '../../src/core/migrate.ts';
+
+const DATABASE_URL = process.env.DATABASE_URL;
+const skip = !DATABASE_URL;
+
+describe.skipIf(skip)('PostgresEngine forward-reference bootstrap (E2E)', () => {
+  let engine: PostgresEngine;
+
+  beforeAll(async () => {
+    engine = new PostgresEngine();
+    await engine.connect({ database_url: DATABASE_URL! });
+  });
+
+  afterAll(async () => {
+    await engine.disconnect();
+  });
+
+  test('PostgresEngine.initSchema applies bootstrap → SCHEMA_SQL → migrations on pre-v0.18 brain', async () => {
+    // First call: bring the test DB to LATEST shape so we have something to mutate.
+    await engine.initSchema();
+
+    // Clear data from prior tests in the suite. Adding a UNIQUE(slug)
+    // constraint below would fail if multi-source fixtures left rows with
+    // duplicate slugs across sources (which is valid under the composite
+    // UNIQUE this test is undoing).
+    const conn = (engine as any).sql;
+    await conn.unsafe(`TRUNCATE pages, content_chunks, links, tags, raw_data, timeline_entries, page_versions, ingest_log RESTART IDENTITY CASCADE`);
+
+    // Mutate to pre-v0.18 shape: drop source_id and the sources table.
+    // The advisory lock is released between initSchema calls, so this
+    // direct DDL won't deadlock.
+    await conn.unsafe(`
+      ALTER TABLE pages DROP CONSTRAINT IF EXISTS pages_source_slug_key;
+      ALTER TABLE pages ADD CONSTRAINT pages_slug_key UNIQUE (slug);
+      DROP INDEX IF EXISTS idx_pages_source_id;
+      ALTER TABLE pages DROP COLUMN IF EXISTS source_id CASCADE;
+      DROP TABLE IF EXISTS sources CASCADE;
+    `);
+    await engine.setConfig('version', '20');
+
+    // The path under test: full PostgresEngine.initSchema() including the
+    // bootstrap call, SCHEMA_SQL replay, and runMigrations chain.
+    await engine.initSchema();
+
+    expect(await engine.getConfig('version')).toBe(String(LATEST_VERSION));
+
+    // Verify the forward-referenced column exists after upgrade.
+    const colCheck = await conn`
+      SELECT column_name FROM information_schema.columns
+      WHERE table_schema = current_schema()
+        AND table_name = 'pages'
+        AND column_name = 'source_id'
+    `;
+    expect(colCheck).toHaveLength(1);
+
+    // Verify the default source row was seeded.
+    const srcCheck = await conn`SELECT id FROM sources WHERE id = 'default'`;
+    expect(srcCheck).toHaveLength(1);
+  });
+
+  test('PostgresEngine.initSchema is idempotent on a brain already at LATEST', async () => {
+    // Fresh-LATEST brain. Calling initSchema again must not error and must
+    // not regress the version.
+    await engine.initSchema();
+    expect(await engine.getConfig('version')).toBe(String(LATEST_VERSION));
+  });
+});

test/e2e/storage-tiering.test.ts

@@ -0,0 +1,273 @@
+/**
+ * E2E test for storage tiering — Postgres-only.
+ *
+ * Per the v0.23.0 plan: full lifecycle. Container restart simulation:
+ * write pages via Postgres, delete files from disk, run gbrain export
+ * --restore-only, assert files restored. Real .gitignore round-trip.
+ * Real source-resolver path through getDefaultSourcePath().
+ *
+ * Skips gracefully when DATABASE_URL is unset (per CLAUDE.md E2E pattern).
+ */
+
+import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
+import { mkdtempSync, rmSync, writeFileSync, readFileSync, existsSync, mkdirSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { setupDB, teardownDB, getEngine, hasDatabase, getConn } from './helpers.ts';
+import {
+  getStorageStatus,
+  formatStorageStatusHuman,
+  __resetPGLiteWarn,
+} from '../../src/commands/storage.ts';
+import { manageGitignore, __resetPGLiteTierWarn } from '../../src/commands/sync.ts';
+import { getDefaultSourcePath } from '../../src/core/source-resolver.ts';
+import { __resetMissingStorageWarning } from '../../src/core/storage-config.ts';
+
+if (!hasDatabase()) {
+  describe('storage-tiering E2E', () => {
+    test.skip('DATABASE_URL not set — skipping E2E', () => {});
+  });
+} else {
+  describe('storage-tiering E2E (Postgres lifecycle)', () => {
+    let tmp: string;
+
+    beforeAll(async () => {
+      await setupDB();
+    });
+
+    afterAll(async () => {
+      await teardownDB();
+    });
+
+    beforeEach(() => {
+      tmp = mkdtempSync(join(tmpdir(), 'gbrain-e2e-storage-'));
+      __resetMissingStorageWarning();
+      __resetPGLiteWarn();
+      __resetPGLiteTierWarn();
+    });
+
+    function cleanup(): void {
+      rmSync(tmp, { recursive: true, force: true });
+    }
+
+    function writeGbrainYml(): void {
+      writeFileSync(
+        join(tmp, 'gbrain.yml'),
+        `storage:
+  db_tracked:
+    - people/
+  db_only:
+    - media/x/
+    - media/articles/
+`,
+      );
+    }
+
+    test('engine.kind is postgres', () => {
+      try {
+        expect(getEngine().kind).toBe('postgres');
+      } finally {
+        cleanup();
+      }
+    });
+
+    test('full lifecycle: write pages → status reports tiers → manage .gitignore → restore-only path', async () => {
+      try {
+        const engine = getEngine();
+
+        // Truncate sources + pages so this test has a clean slate.
+        const conn = getConn();
+        await conn.unsafe(`TRUNCATE pages, content_chunks, sources CASCADE`);
+        await conn.unsafe(
+          `INSERT INTO sources (id, name, local_path) VALUES ('default', 'Default', $1)`,
+          [tmp],
+        );
+
+        writeGbrainYml();
+
+        // Seed 4 pages: 1 db_tracked, 2 db_only, 1 unspecified.
+        await engine.putPage('people/alice', {
+          type: 'person',
+          title: 'Alice',
+          compiled_truth: 'Alice is a founder.',
+          timeline: '',
+        });
+        await engine.putPage('media/x/tweet-1', {
+          type: 'media',
+          title: 'Tweet 1',
+          compiled_truth: 'tweet body',
+          timeline: '',
+        });
+        await engine.putPage('media/x/tweet-2', {
+          type: 'media',
+          title: 'Tweet 2',
+          compiled_truth: 'tweet body 2',
+          timeline: '',
+        });
+        await engine.putPage('random/note', {
+          type: 'note',
+          title: 'Random',
+          compiled_truth: 'random',
+          timeline: '',
+        });
+
+        // Storage status reports tier counts correctly.
+        const status = await getStorageStatus(engine, tmp);
+        expect(status.totalPages).toBe(4);
+        expect(status.pagesByTier.db_tracked).toBe(1);
+        expect(status.pagesByTier.db_only).toBe(2);
+        expect(status.pagesByTier.unspecified).toBe(1);
+
+        // Human formatter renders without errors.
+        const out = formatStorageStatusHuman(status);
+        expect(out).toContain('DB tracked:     1 pages');
+        expect(out).toContain('DB only:        2 pages');
+
+        // .gitignore management: empty .gitignore → managed block written.
+        manageGitignore(tmp, 'postgres');
+        const gitignore = readFileSync(join(tmp, '.gitignore'), 'utf-8');
+        expect(gitignore).toContain('# Auto-managed by gbrain');
+        expect(gitignore).toContain('media/x/');
+        expect(gitignore).toContain('media/articles/');
+
+        // Idempotency: second run adds nothing new.
+        manageGitignore(tmp, 'postgres');
+        const gitignore2 = readFileSync(join(tmp, '.gitignore'), 'utf-8');
+        const xCount = (gitignore2.match(/^media\/x\/$/gm) || []).length;
+        expect(xCount).toBe(1);
+
+        // Source resolution finds the local_path we registered.
+        const resolvedPath = await getDefaultSourcePath(engine);
+        expect(resolvedPath).toBe(tmp);
+      } finally {
+        cleanup();
+      }
+    });
+
+    test('container restart simulation: db_only files missing on disk are restorable from DB', async () => {
+      try {
+        const engine = getEngine();
+        const conn = getConn();
+
+        // Fresh slate.
+        await conn.unsafe(`TRUNCATE pages, content_chunks, sources CASCADE`);
+        await conn.unsafe(
+          `INSERT INTO sources (id, name, local_path) VALUES ('default', 'Default', $1)`,
+          [tmp],
+        );
+
+        writeGbrainYml();
+
+        // Write some db_only pages to the database.
+        await engine.putPage('media/x/tweet-1', {
+          type: 'media',
+          title: 'Tweet 1',
+          compiled_truth: 'tweet body 1',
+          timeline: '',
+        });
+        await engine.putPage('media/x/tweet-2', {
+          type: 'media',
+          title: 'Tweet 2',
+          compiled_truth: 'tweet body 2',
+          timeline: '',
+        });
+
+        // Simulate "files were on disk, but the container restarted."
+        // Storage status: missingFiles should list them.
+        const status = await getStorageStatus(engine, tmp);
+        expect(status.pagesByTier.db_only).toBe(2);
+        expect(status.missingFiles.length).toBe(2);
+
+        // Verify slugPrefix engine filter (Issue #13) works on Postgres for
+        // the prefix that --restore-only would use.
+        const tierPages = await engine.listPages({ slugPrefix: 'media/x/', limit: 100 });
+        expect(tierPages.map((p) => p.slug).sort()).toEqual(['media/x/tweet-1', 'media/x/tweet-2']);
+
+        // Source-default path resolution returns the configured local_path
+        // (the typed accessor that replaces the original raw-SQL try/catch
+        // in storage.ts:38).
+        const path = await getDefaultSourcePath(engine);
+        expect(path).toBe(tmp);
+      } finally {
+        cleanup();
+      }
+    });
+
+    test('slugPrefix filter on Postgres uses index-based range scan (regression for Issue #13)', async () => {
+      try {
+        const engine = getEngine();
+        const conn = getConn();
+        await conn.unsafe(`TRUNCATE pages, content_chunks, sources CASCADE`);
+        await conn.unsafe(`INSERT INTO sources (id, name) VALUES ('default', 'Default')`);
+
+        // Seed enough data to make a difference between scan types.
+        for (let i = 0; i < 50; i++) {
+          await engine.putPage(`media/x/item-${i}`, {
+            type: 'media',
+            title: `Item ${i}`,
+            compiled_truth: 'x',
+            timeline: '',
+          });
+        }
+        for (let i = 0; i < 50; i++) {
+          await engine.putPage(`people/p-${i}`, {
+            type: 'person',
+            title: `Person ${i}`,
+            compiled_truth: 'x',
+            timeline: '',
+          });
+        }
+
+        // Prefix query should return exactly 50 (people not included).
+        const xResults = await engine.listPages({ slugPrefix: 'media/x/', limit: 200 });
+        expect(xResults.length).toBe(50);
+        for (const p of xResults) {
+          expect(p.slug.startsWith('media/x/')).toBe(true);
+        }
+
+        // Path-segment risk: slugPrefix 'media/x' (no /) would match
+        // 'media/xerox' if any existed. The engine treats slugPrefix as a
+        // literal string prefix; trailing-/ semantics are the matcher's
+        // responsibility (storage-config.ts).
+        const looseResults = await engine.listPages({ slugPrefix: 'media/x', limit: 200 });
+        expect(looseResults.length).toBe(50); // no media/xerox/* exists yet
+      } finally {
+        cleanup();
+      }
+    });
+
+    test('hard-error path: storage status without local_path or --repo gets null repoPath', async () => {
+      try {
+        const engine = getEngine();
+        const conn = getConn();
+        await conn.unsafe(`TRUNCATE sources CASCADE`);
+        // Default source with NO local_path.
+        await conn.unsafe(
+          `INSERT INTO sources (id, name, local_path) VALUES ('default', 'Default', NULL)`,
+        );
+
+        const path = await getDefaultSourcePath(engine);
+        expect(path).toBeNull();
+      } finally {
+        cleanup();
+      }
+    });
+
+    test('manageGitignore on Postgres engine does NOT emit PGLite warning', async () => {
+      try {
+        writeGbrainYml();
+        const warnings: string[] = [];
+        const orig = console.warn;
+        console.warn = (...a: unknown[]) => warnings.push(a.map(String).join(' '));
+        try {
+          manageGitignore(tmp, 'postgres');
+        } finally {
+          console.warn = orig;
+        }
+        expect(warnings.filter((w) => /limited effect on PGLite/.test(w))).toEqual([]);
+      } finally {
+        cleanup();
+      }
+    });
+  });
+}

test/e2e/sync-parallel.test.ts

@@ -0,0 +1,167 @@
+/**
+ * E2E test for parallel sync against real Postgres.
+ *
+ *   T2 — happy path: 60-file sync at concurrency=4 against PostgresEngine
+ *        actually constructs N worker engines, imports correctly, and does
+ *        not leak connections (probe pg_stat_activity before/after).
+ *   P4 — benchmark: serial vs concurrency=4 timing on the same fixture so
+ *        the v0.22.13 CHANGELOG can quote a real number instead of "~4×".
+ *
+ * Gated on DATABASE_URL. Run via:
+ *   docker run -d --name gbrain-test-pg -e POSTGRES_USER=postgres \
+ *     -e POSTGRES_PASSWORD=postgres -e POSTGRES_DB=gbrain_test \
+ *     -p 5435:5432 pgvector/pgvector:pg16
+ *   DATABASE_URL=postgresql://postgres:postgres@localhost:5435/gbrain_test \
+ *     bun test test/e2e/sync-parallel.test.ts
+ */
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import { mkdtempSync, rmSync, writeFileSync, mkdirSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { execSync } from 'child_process';
+import { hasDatabase, setupDB, teardownDB, getEngine, getConn } from './helpers.ts';
+
+const skip = !hasDatabase();
+const describeE2E = skip ? describe.skip : describe;
+
+if (skip) {
+  console.log('Skipping E2E sync-parallel tests (DATABASE_URL not set)');
+}
+
+function seedRepo(repoPath: string, fileCount: number): string {
+  execSync('git init', { cwd: repoPath, stdio: 'pipe' });
+  execSync('git config user.email "test@test.com"', { cwd: repoPath, stdio: 'pipe' });
+  execSync('git config user.name "Test"', { cwd: repoPath, stdio: 'pipe' });
+  mkdirSync(join(repoPath, 'people'), { recursive: true });
+  for (let i = 0; i < fileCount; i++) {
+    writeFileSync(join(repoPath, `people/p${i}.md`), [
+      '---',
+      'type: person',
+      `title: Person ${i}`,
+      '---',
+      '',
+      `Person ${i} body — some text long enough to chunk.`,
+      `Iteration index ${i}, generated by sync-parallel E2E.`,
+    ].join('\n'));
+  }
+  execSync('git add -A && git commit -m "initial"', { cwd: repoPath, stdio: 'pipe' });
+  return execSync('git rev-parse HEAD', { cwd: repoPath, encoding: 'utf-8' }).trim();
+}
+
+async function activeConnections(): Promise<number> {
+  const conn = getConn();
+  const rows = await conn.unsafe(`
+    SELECT count(*) AS n FROM pg_stat_activity
+    WHERE datname = current_database()
+      AND state IS NOT NULL
+  `) as Array<{ n: string }>;
+  return parseInt(rows[0]?.n ?? '0', 10);
+}
+
+describeE2E('E2E sync-parallel: T2 happy path + leak probe', () => {
+  let repoPath: string;
+
+  beforeAll(async () => {
+    await setupDB();
+  });
+
+  afterAll(async () => {
+    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
+    await teardownDB();
+  });
+
+  test('60-file Postgres sync at concurrency=4 imports all + no connection leak', async () => {
+    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-e2e-par-'));
+    seedRepo(repoPath, 60);
+
+    const before = await activeConnections();
+
+    const { performSync } = await import('../../src/commands/sync.ts');
+    const engine = getEngine();
+    const result = await performSync(engine, {
+      repoPath,
+      noPull: true,
+      noEmbed: true,
+      concurrency: 4,
+    });
+
+    // First sync routes through performFullSync (delegates to runImport which
+    // also accepts --workers); status is 'first_sync'.
+    expect(result.status).toBe('first_sync');
+
+    const after = await activeConnections();
+
+    // Allow some slack — the helper engine + sync's normal pool stay open.
+    // Worker engines (4 × 2 = 8 connections) MUST have closed; if they
+    // hadn't, after - before would be at least 8.
+    expect(after - before).toBeLessThan(4);
+
+    // Verify pages are actually in the DB (via raw SQL — engine API also works).
+    const conn = getConn();
+    const pageRows = await conn.unsafe(
+      `SELECT count(*) AS n FROM pages WHERE slug LIKE 'people/p%'`,
+    ) as Array<{ n: string }>;
+    const count = parseInt(pageRows[0]?.n ?? '0', 10);
+    expect(count).toBe(60);
+  }, 60_000);
+});
+
+describeE2E('E2E sync-parallel: P4 benchmark serial vs concurrency=4', () => {
+  let repoSerial: string;
+  let repoParallel: string;
+
+  beforeAll(async () => {
+    await setupDB();
+  });
+
+  afterAll(async () => {
+    if (repoSerial) rmSync(repoSerial, { recursive: true, force: true });
+    if (repoParallel) rmSync(repoParallel, { recursive: true, force: true });
+    await teardownDB();
+  });
+
+  test('120-file benchmark: report serial and parallel wall-clock', async () => {
+    // Two separate repos so neither sync's chunks bleed into the other.
+    repoSerial = mkdtempSync(join(tmpdir(), 'gbrain-bench-serial-'));
+    repoParallel = mkdtempSync(join(tmpdir(), 'gbrain-bench-parallel-'));
+    seedRepo(repoSerial, 120);
+    seedRepo(repoParallel, 120);
+
+    const { performSync } = await import('../../src/commands/sync.ts');
+    const engine = getEngine();
+
+    // Truncate between runs to keep the benchmark honest.
+    const conn = getConn();
+
+    const t1 = Date.now();
+    await performSync(engine, {
+      repoPath: repoSerial,
+      noPull: true,
+      noEmbed: true,
+      concurrency: 1,
+    });
+    const serialMs = Date.now() - t1;
+
+    // Wipe pages before second run so neither one is "incremental".
+    await conn.unsafe(`TRUNCATE pages CASCADE`);
+    await conn.unsafe(`TRUNCATE config CASCADE`);
+
+    const t2 = Date.now();
+    await performSync(engine, {
+      repoPath: repoParallel,
+      noPull: true,
+      noEmbed: true,
+      concurrency: 4,
+    });
+    const parallelMs = Date.now() - t2;
+
+    const speedup = (serialMs / parallelMs).toFixed(2);
+    // Emit as a single line stdout consumers can grep for.
+    console.log(`SYNC_PARALLEL_BENCH 120 files | serial=${serialMs}ms | parallel(4)=${parallelMs}ms | speedup=${speedup}x`);
+
+    // Soft assertion: parallel must not be slower than serial. The actual
+    // speedup ratio depends heavily on Postgres latency profile and is what
+    // the CHANGELOG quotes — don't gate the test on a specific multiplier.
+    expect(parallelMs).toBeLessThanOrEqual(serialMs * 1.5); // +50% slack for noisy CI
+  }, 120_000);
+});

test/e2e/sync.test.ts

@@ -10,10 +10,10 @@
  */
 
 import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
-import { mkdtempSync, writeFileSync, rmSync, mkdirSync, unlinkSync } from 'fs';
+import { mkdtempSync, writeFileSync, rmSync, mkdirSync, unlinkSync, existsSync, readFileSync } from 'fs';
 import { join } from 'path';
 import { execSync } from 'child_process';
-import { tmpdir } from 'os';
+import { tmpdir, homedir } from 'os';
 import {
   hasDatabase, setupDB, teardownDB, getEngine,
 } from './helpers.ts';
@@ -394,3 +394,163 @@ describeE2E('E2E: Git-to-DB Sync Pipeline', () => {
     expect(page!.title).toBe('Draft Meeting Notes');
   });
 });
+
+/**
+ * E2E: --skip-failed loop with structured error code summary.
+ *
+ * Closes the v0.22.12 ship-blocker gap from issue #500 — the whole code path
+ * (record → classify → block → skip → doctor render → second cycle) had only
+ * mocked-JSONL unit coverage. This is the integration test that proves the
+ * chain holds together with a real Postgres engine, real git history, and
+ * real frontmatter validation.
+ *
+ * Owns its own repo + sync-failures.jsonl lifecycle so it can't leak state
+ * into the shared describeE2E above. Saves and restores the user's real
+ * ~/.gbrain/sync-failures.jsonl so running E2E on a developer machine
+ * doesn't trash their local sync state.
+ */
+describeE2E('E2E: sync --skip-failed structured summary loop (v0.22.12, issue #500)', () => {
+  let repoPath: string;
+  const realFailuresPath = join(homedir(), '.gbrain', 'sync-failures.jsonl');
+  let savedFailuresContent: string | null = null;
+
+  beforeAll(async () => {
+    await setupDB();
+
+    // Save+clear the real ~/.gbrain/sync-failures.jsonl so the test starts from
+    // a known-empty state. Restored in afterAll. This file is per-machine, NOT
+    // per-repo, so we have to be defensive about a developer running this
+    // suite on their actual brain machine.
+    if (existsSync(realFailuresPath)) {
+      savedFailuresContent = readFileSync(realFailuresPath, 'utf-8');
+      unlinkSync(realFailuresPath);
+    }
+
+    // Fresh git repo with one valid file. Mirrors createTestRepo above but
+    // scoped to this describe block.
+    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-skipfailed-e2e-'));
+    execSync('git init', { cwd: repoPath, stdio: 'pipe' });
+    execSync('git config user.email "test@test.com"', { cwd: repoPath, stdio: 'pipe' });
+    execSync('git config user.name "Test"', { cwd: repoPath, stdio: 'pipe' });
+    mkdirSync(join(repoPath, 'people'), { recursive: true });
+    writeFileSync(join(repoPath, 'people/alice.md'), [
+      '---', 'type: person', 'title: Alice', '---', '', 'Body.',
+    ].join('\n'));
+    execSync('git add -A && git commit -m "initial"', { cwd: repoPath, stdio: 'pipe' });
+  });
+
+  afterAll(async () => {
+    await teardownDB();
+    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
+
+    // Restore the user's real sync-failures.jsonl, if any.
+    if (savedFailuresContent !== null) {
+      mkdirSync(join(homedir(), '.gbrain'), { recursive: true });
+      writeFileSync(realFailuresPath, savedFailuresContent);
+    } else if (existsSync(realFailuresPath)) {
+      // Test wrote one but there was none before. Clean up.
+      unlinkSync(realFailuresPath);
+    }
+  });
+
+  test('full --skip-failed loop: blocks on bad file, skip advances bookmark, doctor shows code breakdown', async () => {
+    const { performSync } = await import('../../src/commands/sync.ts');
+    const { loadSyncFailures, summarizeFailuresByCode } = await import('../../src/core/sync.ts');
+    const engine = getEngine();
+
+    // Step 1: First sync of the clean repo — should succeed.
+    let result = await performSync(engine, { repoPath, noPull: true, noEmbed: true });
+    expect(result.status).toBe('first_sync');
+    const firstCommit = await engine.getConfig('sync.last_commit');
+    expect(firstCommit).toBeTruthy();
+
+    // Step 2: Add a broken file — frontmatter slug doesn't match path-derived slug.
+    // The file path is people/bob.md so the path-derived slug is "people/bob",
+    // but we declare slug: "wrong-slug" in frontmatter. import-file.ts:368-377
+    // raises "Frontmatter slug ... does not match path-derived slug ..." which
+    // classifier hits as SLUG_MISMATCH.
+    writeFileSync(join(repoPath, 'people/bob.md'), [
+      '---', 'type: person', 'title: Bob', 'slug: wrong-slug', '---', '', 'Body.',
+    ].join('\n'));
+    execSync('git add -A && git commit -m "add broken bob"', { cwd: repoPath, stdio: 'pipe' });
+
+    // Step 3: Sync should block. Bookmark must NOT advance.
+    result = await performSync(engine, { repoPath, noPull: true, noEmbed: true });
+    expect(result.status).toBe('blocked_by_failures');
+    const afterBlockedCommit = await engine.getConfig('sync.last_commit');
+    expect(afterBlockedCommit).toBe(firstCommit); // bookmark stuck at the pre-broken commit
+
+    // JSONL has one unacked entry with code SLUG_MISMATCH.
+    let failures = loadSyncFailures();
+    expect(failures.length).toBe(1);
+    expect(failures[0].code).toBe('SLUG_MISMATCH');
+    expect(failures[0].acknowledged).toBeFalsy();
+    // Group summary aggregates correctly across the unacked set.
+    expect(summarizeFailuresByCode(failures)).toEqual([{ code: 'SLUG_MISMATCH', count: 1 }]);
+
+    // Step 4: Run with skipFailed — bookmark advances, entry gets acked.
+    result = await performSync(engine, { repoPath, noPull: true, noEmbed: true, skipFailed: true });
+    expect(result.status).toBe('synced');
+    const afterSkipCommit = await engine.getConfig('sync.last_commit');
+    expect(afterSkipCommit).not.toBe(firstCommit); // bookmark moved past the broken commit
+    failures = loadSyncFailures();
+    expect(failures.length).toBe(1);
+    expect(failures[0].acknowledged).toBe(true);
+    expect(typeof failures[0].acknowledged_at).toBe('string');
+
+    // Step 5: Verify what doctor would render for the historical entry.
+    // We call the same primitives doctor's `sync_failures` check uses
+    // (src/commands/doctor.ts:252-275) — loadSyncFailures + summarizeFailuresByCode —
+    // and assert the rendering string. Directly invoking runDoctor() here is a CLI
+    // entrypoint with stdout/exit side effects that would truncate this test mid-flow.
+    {
+      const all = loadSyncFailures();
+      const ackedSummary = summarizeFailuresByCode(all);
+      const ackedBreakdown = ackedSummary.map(s => `${s.code}=${s.count}`).join(', ');
+      // This is the literal string interpolation doctor.ts:271-274 produces.
+      const doctorMessage = `${all.length} historical sync failure(s), all acknowledged [${ackedBreakdown}].`;
+      expect(doctorMessage).toContain('SLUG_MISMATCH=1');
+      expect(doctorMessage).toContain('1 historical');
+    }
+
+    // Step 6: Add a second broken file — this one with a different failure code
+    // (also SLUG_MISMATCH but on a different file) so the JSONL has 2 entries
+    // with DIFFERENT paths but the same code. This proves both: per-file dedup
+    // honors path identity, and summary aggregation sums across files.
+    //
+    // We'd ideally test a different code class here, but the sync path uses
+    // parseMarkdown WITHOUT {validate:true}, so the markdown.ts validation
+    // codes (MISSING_OPEN/CLOSE, NESTED_QUOTES, EMPTY_FRONTMATTER, NULL_BYTES)
+    // don't naturally surface — they'd need {validate:true} plumbed in. That
+    // plumbing is the v0.22.13+ follow-up. For v0.22.12, two SLUG_MISMATCH
+    // entries from different files still proves the dedup + aggregation chain.
+    writeFileSync(join(repoPath, 'people/carol.md'), [
+      '---', 'type: person', 'title: Carol', 'slug: also-wrong-slug', '---', '', 'Body.',
+    ].join('\n'));
+    execSync('git add -A && git commit -m "add carol with bad slug"', { cwd: repoPath, stdio: 'pipe' });
+
+    // Step 7: Sync blocks again on the new failure. Old entry stays acked.
+    result = await performSync(engine, { repoPath, noPull: true, noEmbed: true });
+    expect(result.status).toBe('blocked_by_failures');
+    failures = loadSyncFailures();
+    expect(failures.length).toBe(2);
+    const acked = failures.filter(f => f.acknowledged);
+    const unacked = failures.filter(f => !f.acknowledged);
+    expect(acked.length).toBe(1);
+    expect(acked[0].code).toBe('SLUG_MISMATCH');
+    expect(acked[0].path).toContain('bob');
+    expect(unacked.length).toBe(1);
+    expect(unacked[0].code).toBe('SLUG_MISMATCH');
+    expect(unacked[0].path).toContain('carol');
+
+    // Step 8: Skip again — both entries acked, summary aggregates the count.
+    result = await performSync(engine, { repoPath, noPull: true, noEmbed: true, skipFailed: true });
+    expect(result.status).toBe('synced');
+    failures = loadSyncFailures();
+    expect(failures.length).toBe(2);
+    expect(failures.every(f => f.acknowledged)).toBe(true);
+
+    const finalSummary = summarizeFailuresByCode(failures);
+    expect(finalSummary).toEqual([{ code: 'SLUG_MISMATCH', count: 2 }]);
+  });
+});

test/extract-incremental.test.ts

@@ -7,28 +7,39 @@
  *
  * All tests use PGLite/in-memory — no DB connection required.
  */
-import { describe, test, expect, beforeEach, afterEach } from 'bun:test';
+import { describe, test, expect, beforeAll, afterAll, beforeEach, afterEach } from 'bun:test';
 import { mkdtempSync, writeFileSync, mkdirSync, rmSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
 import { runExtractCore } from '../src/commands/extract.ts';
 import { PGLiteEngine } from '../src/core/pglite-engine.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
+import { resetPgliteState } from './helpers/reset-pglite.ts';
 
+// One PGLite per file (beforeAll), wipe data per test (beforeEach).
+// PGLite cold-start dominates wall-time; sharing the engine across all tests
+// in this file cuts ~22s × 8 tests = ~3 min on CI.
 let engine: PGLiteEngine;
 let tempDir: string;
 
-beforeEach(async () => {
+beforeAll(async () => {
   engine = new PGLiteEngine();
   await engine.connect({ engine: 'pglite' });
   await engine.initSchema();
+});
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+beforeEach(async () => {
+  await resetPgliteState(engine);
   tempDir = mkdtempSync(join(tmpdir(), 'gbrain-extract-test-'));
   mkdirSync(join(tempDir, 'people'), { recursive: true });
   mkdirSync(join(tempDir, 'companies'), { recursive: true });
 });
 
-afterEach(async () => {
-  await engine.disconnect();
+afterEach(() => {
   rmSync(tempDir, { recursive: true, force: true });
 });
 

test/handlers.test.ts

@@ -120,3 +120,105 @@ describe('autopilot-cycle handler — partial failure does NOT throw', () => {
     }
   }, 30_000);
 });
+
+describe('autopilot-cycle handler — phase passthrough', () => {
+  test('job.data.phases restricts which phases run', async () => {
+    const fs = await import('fs');
+    const { execSync } = await import('child_process');
+    const { tmpdir } = await import('os');
+    const { join } = await import('path');
+    const dir = fs.mkdtempSync(join(tmpdir(), 'gbrain-phase-pass-'));
+    try {
+      execSync('git init', { cwd: dir, stdio: 'pipe' });
+      execSync('git config user.email test@example.com', { cwd: dir, stdio: 'pipe' });
+      execSync('git config user.name Test', { cwd: dir, stdio: 'pipe' });
+      execSync('git commit --allow-empty -m init', { cwd: dir, stdio: 'pipe' });
+
+      const handler = (worker as any).handlers.get('autopilot-cycle');
+      // Request only lint and sync — embed should NOT appear
+      const result = await handler({
+        data: { repoPath: dir, phases: ['lint', 'sync'] },
+        signal: { aborted: false } as any,
+        job: { id: 10, name: 'autopilot-cycle' } as any,
+      });
+
+      expect(result).toBeDefined();
+      const report = (result as any).report;
+      expect(report).toBeDefined();
+      const phaseNames = report.phases.map((p: any) => p.phase);
+      expect(phaseNames).toContain('lint');
+      expect(phaseNames).toContain('sync');
+      // Phases NOT requested must be absent
+      expect(phaseNames).not.toContain('embed');
+      expect(phaseNames).not.toContain('extract');
+      expect(phaseNames).not.toContain('backlinks');
+      expect(phaseNames).not.toContain('orphans');
+    } finally {
+      fs.rmSync(dir, { recursive: true, force: true });
+    }
+  }, 30_000);
+
+  test('invalid phase names in job.data.phases are filtered out', async () => {
+    const fs = await import('fs');
+    const { execSync } = await import('child_process');
+    const { tmpdir } = await import('os');
+    const { join } = await import('path');
+    const dir = fs.mkdtempSync(join(tmpdir(), 'gbrain-phase-invalid-'));
+    try {
+      execSync('git init', { cwd: dir, stdio: 'pipe' });
+      execSync('git config user.email test@example.com', { cwd: dir, stdio: 'pipe' });
+      execSync('git config user.name Test', { cwd: dir, stdio: 'pipe' });
+      execSync('git commit --allow-empty -m init', { cwd: dir, stdio: 'pipe' });
+
+      const handler = (worker as any).handlers.get('autopilot-cycle');
+      // Mix valid and bogus names — only 'lint' should survive filtering
+      const result = await handler({
+        data: { repoPath: dir, phases: ['lint', 'BOGUS', 'rm -rf /'] },
+        signal: { aborted: false } as any,
+        job: { id: 11, name: 'autopilot-cycle' } as any,
+      });
+
+      const report = (result as any).report;
+      const phaseNames = report.phases.map((p: any) => p.phase);
+      expect(phaseNames).toContain('lint');
+      expect(phaseNames).not.toContain('BOGUS');
+      expect(phaseNames.length).toBe(1);
+    } finally {
+      fs.rmSync(dir, { recursive: true, force: true });
+    }
+  }, 30_000);
+
+  test('empty phases array falls back to all phases (same as no phases)', async () => {
+    const handler = (worker as any).handlers.get('autopilot-cycle');
+    // Empty array should fall through to ALL_PHASES (same as omitting phases)
+    const result = await handler({
+      data: { repoPath: '/definitely-does-not-exist-for-phase-test', phases: [] },
+      signal: { aborted: false } as any,
+      job: { id: 12, name: 'autopilot-cycle' } as any,
+    });
+
+    const report = (result as any).report;
+    // With all phases, filesystem phases fail on missing dir
+    const phaseNames = report.phases.map((p: any) => p.phase);
+    expect(phaseNames).toContain('lint');
+    expect(phaseNames).toContain('backlinks');
+    expect(phaseNames).toContain('sync');
+  }, 30_000);
+
+  test('non-array phases value is ignored (falls back to all)', async () => {
+    const handler = (worker as any).handlers.get('autopilot-cycle');
+    // String instead of array — should be ignored
+    const result = await handler({
+      data: { repoPath: '/definitely-does-not-exist-for-phase-test', phases: 'lint' },
+      signal: { aborted: false } as any,
+      job: { id: 13, name: 'autopilot-cycle' } as any,
+    });
+
+    const report = (result as any).report;
+    const phaseNames = report.phases.map((p: any) => p.phase);
+    // Should have all phases since the string was ignored
+    expect(phaseNames).toContain('lint');
+    expect(phaseNames).toContain('sync');
+    expect(phaseNames).toContain('embed');
+  }, 30_000);
+});

test/helpers/reset-pglite.ts

@@ -0,0 +1,43 @@
+/**
+ * Wipe per-test data on a connected PGLite engine without dropping the schema.
+ * Used by tests that share one engine across the file (beforeAll) and need a
+ * clean slate per test (beforeEach).
+ *
+ * Why this exists: PGLite WASM cold-start + initSchema() is ~20s on CI runners.
+ * Spinning up a fresh engine per test (the prior beforeEach pattern) multiplies
+ * that across every test in every file. Sharing one engine and wiping data
+ * is two orders of magnitude faster.
+ *
+ * Implementation:
+ *   1. TRUNCATE every public table CASCADE, including `sources` (so tests
+ *      that register their own sources don't leak rows into the next test).
+ *   2. Re-seed the default source row that pages.source_id's DEFAULT FKs
+ *      against. Without this, the next page insert would fail FK validation.
+ *   3. Preserve `schema_version` — it carries the migration ledger that
+ *      initSchema() populates; wiping it would make migration helpers think
+ *      the brain is on v0.
+ *
+ * Identifier-quoted defensively against pathological table names.
+ */
+import type { PGLiteEngine } from '../../src/core/pglite-engine.ts';
+
+const PRESERVE_TABLES = new Set(['schema_version']);
+
+export async function resetPgliteState(engine: PGLiteEngine): Promise<void> {
+  const rows = await engine.executeRaw<{ tablename: string }>(
+    `SELECT tablename FROM pg_tables WHERE schemaname='public'`,
+  );
+  const targets = rows
+    .map(r => r.tablename)
+    .filter(name => !PRESERVE_TABLES.has(name));
+  if (targets.length === 0) return;
+  const quoted = targets.map(t => `"${t.replace(/"/g, '""')}"`).join(', ');
+  await engine.executeRaw(`TRUNCATE ${quoted} RESTART IDENTITY CASCADE`);
+  // Re-seed the default source row that initSchema() inserts. Mirrors the
+  // INSERT in src/core/pglite-schema.ts so the FK target survives reset.
+  await engine.executeRaw(
+    `INSERT INTO sources (id, name, config)
+       VALUES ('default', 'default', '{"federated": true}'::jsonb)
+       ON CONFLICT (id) DO NOTHING`,
+  );
+}

test/http-transport.test.ts

@@ -0,0 +1,519 @@
+/**
+ * Unit tests for src/mcp/http-transport.ts.
+ *
+ * Covers:
+ *   - Auth path (valid, missing header, no Bearer prefix, unknown, revoked, /health bypass)
+ *   - F1+F2+F3 round-trip guards (handler arg order, full OperationContext, param validation)
+ *   - JSON-only response shape (no SSE)
+ *   - CORS default-deny + allowlist
+ *   - Body cap (Content-Length + chunked)
+ *   - Rate limit (token + IP buckets, LRU eviction, TTL prune, /health bypass)
+ *
+ * No DATABASE_URL needed — engine.sql is mocked. E2E coverage of the real Postgres
+ * round-trip lives in test/e2e/http-transport.test.ts.
+ */
+
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import { createHash } from 'crypto';
+import { startHttpTransport } from '../src/mcp/http-transport.ts';
+import { RateLimiter } from '../src/mcp/rate-limit.ts';
+
+type SqlResult = unknown[] | unknown;
+type SqlHandler = (query: string, values: unknown[]) => SqlResult | Promise<SqlResult>;
+
+interface FakeEngine {
+  kind: 'postgres';
+  sql: ReturnType<typeof makeSqlTag>;
+  audit: { token_name: string | null; operation: string; status: string; latency_ms: number }[];
+}
+
+function makeSqlTag(handler: SqlHandler) {
+  return (strings: TemplateStringsArray, ...values: unknown[]) => {
+    let query = '';
+    for (let i = 0; i < strings.length; i++) {
+      query += strings[i];
+      if (i < values.length) query += '?';
+    }
+    const result = handler(query.trim(), values);
+    return Promise.resolve(result);
+  };
+}
+
+function hash(token: string): string {
+  return createHash('sha256').update(token).digest('hex');
+}
+
+interface FakeEngineConfig {
+  validTokens?: Map<string, { id: string; name: string }>;
+  /** Tokens that are present but revoked (revoked_at IS NOT NULL — query returns empty). */
+  revokedTokens?: Set<string>;
+  /** If true, every SELECT throws (simulating DB outage). */
+  dbDown?: boolean;
+}
+
+function makeFakeEngine(cfg: FakeEngineConfig = {}): FakeEngine {
+  const validTokens = cfg.validTokens ?? new Map();
+  const revokedTokens = cfg.revokedTokens ?? new Set();
+  const audit: FakeEngine['audit'] = [];
+
+  const sql = makeSqlTag((query, values) => {
+    if (cfg.dbDown && query.startsWith('SELECT')) throw new Error('db down');
+
+    if (query === 'SELECT 1') {
+      // /health DB probe
+      return [{ '?column?': 1 }];
+    }
+
+    if (query.startsWith('SELECT id, name FROM access_tokens')) {
+      const tokenHash = values[0] as string;
+      if (revokedTokens.has(tokenHash)) return [];
+      const row = validTokens.get(tokenHash);
+      return row ? [row] : [];
+    }
+
+    if (query.startsWith('UPDATE access_tokens')) {
+      // last_used_at debounce — succeed silently
+      return [];
+    }
+
+    if (query.startsWith('INSERT INTO mcp_request_log')) {
+      audit.push({
+        token_name: values[0] as string | null,
+        operation: values[1] as string,
+        latency_ms: values[2] as number,
+        status: values[3] as string,
+      });
+      return [];
+    }
+
+    return [];
+  });
+
+  return { kind: 'postgres', sql, audit };
+}
+
+interface TestServer {
+  url: string;
+  stop: () => void;
+  engine: FakeEngine;
+  ipLimiter: RateLimiter;
+  tokenLimiter: RateLimiter;
+}
+
+let mockNow = 0;
+function freezeClock(at: number) { mockNow = at; }
+function advanceClock(deltaMs: number) { mockNow += deltaMs; }
+
+async function startTest(cfg: FakeEngineConfig & { lruCap?: number; ipLimit?: number; tokenLimit?: number; corsOrigin?: string; bodyCap?: number; trustProxy?: boolean } = {}): Promise<TestServer> {
+  if (cfg.corsOrigin) process.env.GBRAIN_HTTP_CORS_ORIGIN = cfg.corsOrigin;
+  else delete process.env.GBRAIN_HTTP_CORS_ORIGIN;
+  if (cfg.bodyCap) process.env.GBRAIN_HTTP_MAX_BODY_BYTES = String(cfg.bodyCap);
+  else delete process.env.GBRAIN_HTTP_MAX_BODY_BYTES;
+  if (cfg.trustProxy) process.env.GBRAIN_HTTP_TRUST_PROXY = '1';
+  else delete process.env.GBRAIN_HTTP_TRUST_PROXY;
+
+  const engine = makeFakeEngine(cfg);
+  const clock = () => mockNow || Date.now();
+  const ipLimiter = new RateLimiter(
+    { limit: cfg.ipLimit ?? 1000, windowMs: 60_000, lruCap: cfg.lruCap ?? 10000 },
+    clock,
+  );
+  const tokenLimiter = new RateLimiter(
+    { limit: cfg.tokenLimit ?? 1000, windowMs: 60_000, lruCap: cfg.lruCap ?? 10000 },
+    clock,
+  );
+  const server = await startHttpTransport({
+    port: 0,
+    engine: engine as any,
+    limiters: { ip: ipLimiter, token: tokenLimiter },
+  });
+  return {
+    url: `http://localhost:${(server as any).port}`,
+    stop: () => (server as any).stop(true),
+    engine,
+    ipLimiter,
+    tokenLimiter,
+  };
+}
+
+function rpc(method: string, params?: unknown, id: number = 1) {
+  return JSON.stringify({ jsonrpc: '2.0', id, method, ...(params !== undefined ? { params } : {}) });
+}
+
+// --------------------------------------------------------------------------
+// Auth path
+// --------------------------------------------------------------------------
+
+describe('http-transport: auth', () => {
+  let srv: TestServer;
+  const VALID_TOKEN = 'valid-token-abc';
+  const REVOKED_TOKEN = 'revoked-token-xyz';
+
+  beforeAll(async () => {
+    srv = await startTest({
+      validTokens: new Map([[hash(VALID_TOKEN), { id: 'tok-1', name: 'test' }]]),
+      revokedTokens: new Set([hash(REVOKED_TOKEN)]),
+    });
+  });
+  afterAll(() => srv.stop());
+
+  test('1. valid token → 200 + tools/list returns ops', async () => {
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${VALID_TOKEN}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.result.tools).toBeArray();
+    expect(body.result.tools.length).toBeGreaterThan(0);
+    expect(body.jsonrpc).toBe('2.0');
+  });
+
+  test('2. missing Authorization header → 401', async () => {
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    expect(r.status).toBe(401);
+  });
+
+  test('3. header missing Bearer prefix → 401', async () => {
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': VALID_TOKEN, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    expect(r.status).toBe(401);
+  });
+
+  test('4. unknown token → 401', async () => {
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': 'Bearer not-a-real-token', 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    expect(r.status).toBe(401);
+  });
+
+  test('5. revoked token → 401', async () => {
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${REVOKED_TOKEN}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    expect(r.status).toBe(401);
+  });
+
+  test('6. /health → 200 without auth, body has expected fields, probes DB', async () => {
+    const r = await fetch(`${srv.url}/health`);
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.status).toBe('ok');
+    expect(body.transport).toBe('http');
+    expect(body.version).toBeString();
+    expect(body.db).toBe('ok');
+  });
+
+  test('6b. /health → 503 when DB is unreachable', async () => {
+    const dbDownSrv = await startTest({ dbDown: true });
+    try {
+      const r = await fetch(`${dbDownSrv.url}/health`);
+      expect(r.status).toBe(503);
+      const body = await r.json();
+      expect(body.status).toBe('unhealthy');
+      expect(body.db).toBe('unreachable');
+    } finally { dbDownSrv.stop(); }
+  });
+});
+
+// --------------------------------------------------------------------------
+// F1+F2+F3 regression guards (the actual existing-PR bugs)
+// --------------------------------------------------------------------------
+
+describe('http-transport: tools/call dispatch', () => {
+  let srv: TestServer;
+  const TOK = 'tok-fix';
+
+  beforeAll(async () => {
+    srv = await startTest({ validTokens: new Map([[hash(TOK), { id: 'tok-fix-id', name: 'fix' }]]) });
+  });
+  afterAll(() => srv.stop());
+
+  test('7. tools/call with a real op (list_pages) round-trips successfully (F1+F2 guard)', async () => {
+    // list_pages doesn't need real DB rows in this stub — it'll call engine methods we don't mock,
+    // so we expect EITHER a successful tool-result OR an isError result with a meaningful message.
+    // The point is that the handler IS invoked with (ctx, params) order — not (params, ctx).
+    // If F1 regressed, the handler would receive {limit: 1} as ctx and crash trying to read ctx.engine.
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/call', { name: 'list_pages', arguments: { limit: 1 } }),
+    });
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.jsonrpc).toBe('2.0');
+    expect(body.result).toBeDefined();
+    expect(body.result.content).toBeArray();
+    // Either success (handler ran) or a structured error (handler ran and returned an error)
+    // — both prove dispatch reached the handler with the correct shape.
+  });
+
+  test('8. tools/call with malformed params → 200 wrapping an isError result (F3 guard via dispatch.ts)', async () => {
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' },
+      // get_page expects `slug` as required string; passing a number triggers validateParams
+      body: rpc('tools/call', { name: 'get_page', arguments: { slug: 42 } }),
+    });
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.result.isError).toBe(true);
+    const text = body.result.content[0].text;
+    expect(text).toContain('invalid_params');
+  });
+
+  test('9. /mcp response has Content-Type: application/json (not SSE)', async () => {
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/list'),
+    });
+    expect(r.headers.get('content-type')).toContain('application/json');
+    expect(r.headers.get('content-type')).not.toContain('event-stream');
+  });
+
+  test('9b. unknown tool name → 200 wrapping an isError result', async () => {
+    const r = await fetch(`${srv.url}/mcp`, {
+      method: 'POST',
+      headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' },
+      body: rpc('tools/call', { name: 'definitely_not_a_real_tool', arguments: {} }),
+    });
+    expect(r.status).toBe(200);
+    const body = await r.json();
+    expect(body.result.isError).toBe(true);
+    expect(body.result.content[0].text).toContain('Unknown tool');
+  });
+});
+
+// --------------------------------------------------------------------------
+// CORS
+// --------------------------------------------------------------------------
+
+describe('http-transport: CORS', () => {
+  test('10. no GBRAIN_HTTP_CORS_ORIGIN + browser request → no ACAO header', async () => {
+    const srv = await startTest({});
+    try {
+      const r = await fetch(`${srv.url}/health`, { headers: { 'Origin': 'https://evil.example' } });
+      expect(r.headers.get('access-control-allow-origin')).toBeNull();
+    } finally { srv.stop(); }
+  });
+
+  test('11. env set + matching Origin → ACAO echoes', async () => {
+    const srv = await startTest({ corsOrigin: 'https://claude.ai' });
+    try {
+      const r = await fetch(`${srv.url}/health`, { headers: { 'Origin': 'https://claude.ai' } });
+      expect(r.headers.get('access-control-allow-origin')).toBe('https://claude.ai');
+      expect(r.headers.get('vary')).toBe('Origin');
+    } finally { srv.stop(); }
+  });
+
+  test('12. env set + non-matching Origin → no ACAO header', async () => {
+    const srv = await startTest({ corsOrigin: 'https://claude.ai' });
+    try {
+      const r = await fetch(`${srv.url}/health`, { headers: { 'Origin': 'https://evil.example' } });
+      expect(r.headers.get('access-control-allow-origin')).toBeNull();
+    } finally { srv.stop(); }
+  });
+});
+
+// --------------------------------------------------------------------------
+// Body cap
+// --------------------------------------------------------------------------
+
+describe('http-transport: body cap', () => {
+  const TOK = 'body-cap-tok';
+
+  test('13. Content-Length over cap → 413', async () => {
+    const srv = await startTest({
+      validTokens: new Map([[hash(TOK), { id: 'b-1', name: 'b' }]]),
+      bodyCap: 100,
+    });
+    try {
+      const big = 'x'.repeat(200);
+      const r = await fetch(`${srv.url}/mcp`, {
+        method: 'POST',
+        headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' },
+        body: big,
+      });
+      expect(r.status).toBe(413);
+    } finally { srv.stop(); }
+  });
+
+  test('14. chunked transfer (no Content-Length) over cap → 413', async () => {
+    const srv = await startTest({
+      validTokens: new Map([[hash(TOK), { id: 'b-2', name: 'b' }]]),
+      bodyCap: 100,
+    });
+    try {
+      // Build a chunked body via a ReadableStream — Bun fetch sends without Content-Length.
+      const stream = new ReadableStream({
+        start(controller) {
+          for (let i = 0; i < 10; i++) controller.enqueue(new TextEncoder().encode('y'.repeat(50)));
+          controller.close();
+        },
+      });
+      const r = await fetch(`${srv.url}/mcp`, {
+        method: 'POST',
+        headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' },
+        body: stream as any,
+        // @ts-expect-error Bun fetch supports duplex for streaming bodies
+        duplex: 'half',
+      });
+      expect(r.status).toBe(413);
+    } finally { srv.stop(); }
+  });
+});
+
+// --------------------------------------------------------------------------
+// Rate limit
+// --------------------------------------------------------------------------
+
+describe('http-transport: rate limit', () => {
+  const TOK = 'rl-tok';
+
+  test('15. token bucket: refill mechanic over time', async () => {
+    freezeClock(1000);
+    const srv = await startTest({
+      validTokens: new Map([[hash(TOK), { id: 'rl-id', name: 'rl' }]]),
+      tokenLimit: 2,
+      ipLimit: 100,
+    });
+    try {
+      // Use up 2 tokens
+      const ok1 = await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      expect(ok1.status).toBe(200);
+      const ok2 = await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      expect(ok2.status).toBe(200);
+
+      // Third should 429
+      const blocked = await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      expect(blocked.status).toBe(429);
+
+      // Advance past the refill window (60s for 2 limit = 30s/token; advance 35s)
+      advanceClock(35_000);
+      const refilled = await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      expect(refilled.status).toBe(200);
+    } finally { srv.stop(); freezeClock(0); }
+  });
+
+  test('16. token bucket exhausted → 429 + Retry-After header', async () => {
+    freezeClock(1000);
+    const srv = await startTest({
+      validTokens: new Map([[hash(TOK), { id: 'rl16', name: 'rl' }]]),
+      tokenLimit: 1,
+      ipLimit: 100,
+    });
+    try {
+      await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      const r = await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      expect(r.status).toBe(429);
+      expect(r.headers.get('retry-after')).not.toBeNull();
+      expect(parseInt(r.headers.get('retry-after')!, 10)).toBeGreaterThan(0);
+    } finally { srv.stop(); freezeClock(0); }
+  });
+
+  test('17. LRU eviction at cap (insert > cap evicts LRU)', () => {
+    let now = 0;
+    const lim = new RateLimiter({ limit: 10, windowMs: 60_000, lruCap: 3 }, () => now);
+    lim.check('a'); now += 1;
+    lim.check('b'); now += 1;
+    lim.check('c'); now += 1;
+    expect(lim.size).toBe(3);
+    lim.check('d'); now += 1;
+    expect(lim.size).toBe(3);
+    // 'a' should have been evicted (oldest by insertion). After re-checking 'a' it's a fresh bucket again.
+    // Easiest verification: hammer 'a' should NOT be already exhausted — fresh bucket starts at limit.
+    for (let i = 0; i < 10; i++) {
+      const r = lim.check('a');
+      expect(r.allowed).toBe(true);
+    }
+    // 11th should fail (no refill since clock barely moved)
+    expect(lim.check('a').allowed).toBe(false);
+  });
+
+  test('18. TTL prune (entries older than 2× window evicted)', () => {
+    let now = 1000;
+    const lim = new RateLimiter({ limit: 10, windowMs: 1000, lruCap: 100 }, () => now);
+    lim.check('stale'); // touched at t=1000
+    expect(lim.size).toBe(1);
+    now = 1000 + 2001; // advance past 2× window
+    lim.check('fresh'); // triggers prune
+    expect(lim.size).toBe(1); // 'stale' evicted, only 'fresh' remains
+  });
+
+  test('19. pre-auth IP bucket fires BEFORE auth (DB not called when IP exhausted)', async () => {
+    freezeClock(1000);
+    const srv = await startTest({
+      ipLimit: 1,
+      tokenLimit: 100,
+      validTokens: new Map([[hash(TOK), { id: 'rl19', name: 'rl' }]]),
+    });
+    try {
+      // First request consumes IP token (will hit auth and succeed)
+      const r1 = await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      expect(r1.status).toBe(200);
+      // Second: IP bucket exhausted. We send WITHOUT auth header. Should be 429 (IP-limited),
+      // not 401 (auth-failed) — proving IP check happened first.
+      const r2 = await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      expect(r2.status).toBe(429);
+    } finally { srv.stop(); freezeClock(0); }
+  });
+
+  test('20. /health bypasses rate limit', async () => {
+    freezeClock(1000);
+    const srv = await startTest({ ipLimit: 1, tokenLimit: 1 });
+    try {
+      // Hammer health 5 times — none should 429
+      for (let i = 0; i < 5; i++) {
+        const r = await fetch(`${srv.url}/health`);
+        expect(r.status).toBe(200);
+      }
+    } finally { srv.stop(); freezeClock(0); }
+  });
+});
+
+// --------------------------------------------------------------------------
+// mcp_request_log audit
+// --------------------------------------------------------------------------
+
+describe('http-transport: mcp_request_log audit', () => {
+  test('21. successful request → audit row with token_name + operation + status', async () => {
+    const TOK = 'audit-tok';
+    const srv = await startTest({ validTokens: new Map([[hash(TOK), { id: 'a-1', name: 'audit-test' }]]) });
+    try {
+      await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': `Bearer ${TOK}`, 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      // Audit insert is fire-and-forget; give it a tick to land in the fake handler
+      await new Promise(r => setTimeout(r, 10));
+      expect(srv.engine.audit.length).toBeGreaterThanOrEqual(1);
+      const row = srv.engine.audit[srv.engine.audit.length - 1];
+      expect(row.token_name).toBe('audit-test');
+      expect(row.operation).toBe('tools/list');
+      expect(row.status).toBe('success');
+      expect(row.latency_ms).toBeGreaterThanOrEqual(0);
+    } finally { srv.stop(); }
+  });
+
+  test('22. failed auth → audit row with null token_name + auth_failed status', async () => {
+    const srv = await startTest({});
+    try {
+      await fetch(`${srv.url}/mcp`, { method: 'POST', headers: { 'Authorization': 'Bearer wrong', 'Content-Type': 'application/json' }, body: rpc('tools/list') });
+      await new Promise(r => setTimeout(r, 10));
+      expect(srv.engine.audit.length).toBeGreaterThanOrEqual(1);
+      const row = srv.engine.audit[srv.engine.audit.length - 1];
+      expect(row.token_name).toBeNull();
+      expect(row.status).toBe('auth_failed');
+    } finally { srv.stop(); }
+  });
+});

test/migrate.test.ts

@@ -287,6 +287,17 @@ describe('migration v24 — rls_backfill_missing_tables', () => {
   test('LATEST_VERSION has caught up to 24', () => {
     expect(LATEST_VERSION).toBeGreaterThanOrEqual(24);
   });
+
+  // PGLite has no RLS engine and is intrinsically single-tenant. The 8 RLS
+  // backfill ALTER statements target tables that may not exist on PGLite
+  // (subagent_*, minion_inbox aren't always present in pglite-schema.ts).
+  // sqlFor.pglite='' makes v24 a no-op on PGLite while still bumping the
+  // version counter. Engine.kind discrimination in runMigrations selects
+  // sqlFor[engine.kind] over m.sql. Issue #395.
+  test('uses a PGLite no-op override so local brains skip Postgres-only RLS ALTER TABLEs', () => {
+    const v24 = MIGRATIONS.find(m => m.version === 24);
+    expect(v24?.sqlFor?.pglite).toBe('');
+  });
 });
 
 // ─────────────────────────────────────────────────────────────────

test/pglite-engine.test.ts

@@ -101,6 +101,37 @@ describe('PGLiteEngine: Pages', () => {
     expect(tagged[0].slug).toBe('test/tagged');
   });
 
+  test('listPages with slugPrefix filter (Issue #13)', async () => {
+    await truncateAll();
+    await engine.putPage('media/x/tweet-1', { ...testPage, type: 'concept' });
+    await engine.putPage('media/x/tweet-2', { ...testPage, type: 'concept' });
+    await engine.putPage('media/articles/post-1', { ...testPage, type: 'concept' });
+    await engine.putPage('people/alice', { ...testPage, type: 'person' });
+
+    const xOnly = await engine.listPages({ slugPrefix: 'media/x/', limit: 100 });
+    expect(xOnly.map((p) => p.slug).sort()).toEqual(['media/x/tweet-1', 'media/x/tweet-2']);
+
+    const allMedia = await engine.listPages({ slugPrefix: 'media/', limit: 100 });
+    expect(allMedia.length).toBe(3);
+
+    // Path-segment risk: 'media/x' (no trailing /) would also match 'media/xerox'.
+    // The matcher in storage-config.ts is responsible for trailing-/ semantics
+    // (step 6); the engine treats slugPrefix as a literal string prefix.
+    expect((await engine.listPages({ slugPrefix: 'media/x', limit: 100 })).length).toBe(2);
+  });
+
+  test('listPages slugPrefix escapes LIKE metacharacters', async () => {
+    await truncateAll();
+    await engine.putPage('safe/foo', { ...testPage, type: 'concept' });
+    // A user prefix containing % or _ would otherwise match unintended slugs
+    // if not escaped. We can't easily insert a slug with % in it (most slugs
+    // are url-safe), but we can confirm the escape logic doesn't break the
+    // happy path.
+    const result = await engine.listPages({ slugPrefix: 'safe/', limit: 10 });
+    expect(result.length).toBe(1);
+    expect(result[0].slug).toBe('safe/foo');
+  });
+
   test('resolveSlugs exact match', async () => {
     await engine.putPage('test/exact', testPage);
     const slugs = await engine.resolveSlugs('test/exact');

test/schema-bootstrap-coverage.test.ts

@@ -0,0 +1,149 @@
+/**
+ * CI guard: PGLITE_SCHEMA_SQL must not forward-reference state that
+ * `applyForwardReferenceBootstrap` doesn't know how to create.
+ *
+ * Background: gbrain ships an "embedded latest schema" blob
+ * (`pglite-schema.ts`) for fast bootstraps, alongside a numbered migration
+ * chain (`migrate.ts`) for incremental upgrades. Across 2 years and 6 schema
+ * versions, every release that added a column-with-index in the schema blob
+ * without a corresponding bootstrap addition has triggered the same wedge
+ * incident class (#239, #243, #266, #266, #357, #366, #374, #375, #378,
+ * #395, #396).
+ *
+ * The bootstrap is the structural fix. This test enforces the contract:
+ * for every "forward reference" the schema blob makes (FK or indexed column
+ * defined later than its reference site, or any column that older brains
+ * lack), the bootstrap MUST add enough state so that running the schema
+ * blob is replay-safe on a brain that lacks every member of
+ * `REQUIRED_BOOTSTRAP_COVERAGE`.
+ *
+ * **When you add a new schema-blob forward reference:**
+ *   1. Extend `applyForwardReferenceBootstrap` in pglite-engine.ts +
+ *      postgres-engine.ts to add the new state.
+ *   2. Add an entry to `REQUIRED_BOOTSTRAP_COVERAGE` below.
+ *   3. This test will pass.
+ *
+ * If you add a forward reference but skip step 1, this test fails. If you
+ * skip step 2, this test passes but the bootstrap silently drifts behind
+ * the schema. The eng-review polish notes recommended layered coverage
+ * (per-engine integration tests in `test/bootstrap.test.ts` +
+ * `test/e2e/postgres-bootstrap.test.ts`) to catch step 2 oversights.
+ */
+
+import { test, expect } from 'bun:test';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+
+// Forward-reference targets that PGLITE_SCHEMA_SQL requires.
+// When you add a new one, extend this list AND the bootstrap.
+type ForwardReference =
+  | { kind: 'table'; name: string }
+  | { kind: 'column'; table: string; column: string };
+
+const REQUIRED_BOOTSTRAP_COVERAGE: ForwardReference[] = [
+  // Forward-referenced by `pages.source_id REFERENCES sources(id)` and the
+  // `INSERT INTO sources (id, name, config) VALUES ('default', ...)` seed.
+  { kind: 'table',  name: 'sources' },
+  // Forward-referenced by `CREATE INDEX idx_pages_source_id ON pages(source_id)`.
+  { kind: 'column', table: 'pages', column: 'source_id' },
+  // Forward-referenced by `CREATE INDEX idx_links_source ON links(link_source)`.
+  { kind: 'column', table: 'links', column: 'link_source' },
+  // Forward-referenced by `CREATE INDEX idx_links_origin ON links(origin_page_id)`.
+  { kind: 'column', table: 'links', column: 'origin_page_id' },
+  // v0.19+ — forward-referenced by `CREATE INDEX idx_chunks_symbol_name
+  // ON content_chunks(symbol_name) WHERE symbol_name IS NOT NULL`.
+  { kind: 'column', table: 'content_chunks', column: 'symbol_name' },
+  // v0.19+ — forward-referenced by `CREATE INDEX idx_chunks_language
+  // ON content_chunks(language) WHERE language IS NOT NULL`.
+  { kind: 'column', table: 'content_chunks', column: 'language' },
+];
+
+test('applyForwardReferenceBootstrap covers every forward reference declared in REQUIRED_BOOTSTRAP_COVERAGE', async () => {
+  const engine = new PGLiteEngine();
+  await engine.connect({});
+  try {
+    await engine.initSchema();
+    const db = (engine as any).db;
+
+    // Strip every required forward-reference target so the brain looks like
+    // it pre-dates the migrations that introduced these objects. Drop columns
+    // before the table-level constraints that depend on them.
+    await db.exec(`
+      ALTER TABLE pages DROP CONSTRAINT IF EXISTS pages_source_slug_key;
+      ALTER TABLE pages ADD CONSTRAINT pages_slug_key UNIQUE (slug);
+      DROP INDEX IF EXISTS idx_pages_source_id;
+      ALTER TABLE pages DROP COLUMN IF EXISTS source_id;
+      DROP TABLE IF EXISTS sources CASCADE;
+
+      DROP INDEX IF EXISTS idx_links_source;
+      DROP INDEX IF EXISTS idx_links_origin;
+      ALTER TABLE links DROP CONSTRAINT IF EXISTS links_from_to_type_source_origin_unique;
+      ALTER TABLE links DROP COLUMN IF EXISTS link_source;
+      ALTER TABLE links DROP COLUMN IF EXISTS origin_page_id;
+
+      DROP INDEX IF EXISTS idx_chunks_symbol_name;
+      DROP INDEX IF EXISTS idx_chunks_language;
+      ALTER TABLE content_chunks DROP COLUMN IF EXISTS symbol_name;
+      ALTER TABLE content_chunks DROP COLUMN IF EXISTS language;
+    `);
+
+    // Run bootstrap in isolation (NOT initSchema). This is what we're testing.
+    await (engine as any).applyForwardReferenceBootstrap();
+
+    // Assert every required forward-reference target now satisfies the
+    // schema-blob's expectations.
+    for (const ref of REQUIRED_BOOTSTRAP_COVERAGE) {
+      if (ref.kind === 'table') {
+        const { rows } = await db.query(
+          `SELECT 1 FROM information_schema.tables
+           WHERE table_schema = 'public' AND table_name = $1`,
+          [ref.name],
+        );
+        expect(rows.length).toBeGreaterThan(0);
+      } else {
+        const { rows } = await db.query(
+          `SELECT 1 FROM information_schema.columns
+           WHERE table_schema = 'public' AND table_name = $1 AND column_name = $2`,
+          [ref.table, ref.column],
+        );
+        expect(rows.length).toBeGreaterThan(0);
+      }
+    }
+  } finally {
+    await engine.disconnect();
+  }
+}, 30000);
+
+test('after bootstrap, PGLITE_SCHEMA_SQL replays without crashing on missing forward references', async () => {
+  // End-to-end contract: bootstrap → SCHEMA_SQL must succeed even on a brain
+  // that lacks every forward-referenced target. This catches the case where
+  // REQUIRED_BOOTSTRAP_COVERAGE drifts behind PGLITE_SCHEMA_SQL — if the
+  // schema blob added a new index on a column the bootstrap doesn't create,
+  // the SCHEMA_SQL exec below would crash even though the per-target asserts
+  // above pass.
+  const engine = new PGLiteEngine();
+  await engine.connect({});
+  try {
+    await engine.initSchema();
+    const db = (engine as any).db;
+
+    await db.exec(`
+      ALTER TABLE pages DROP CONSTRAINT IF EXISTS pages_source_slug_key;
+      ALTER TABLE pages ADD CONSTRAINT pages_slug_key UNIQUE (slug);
+      DROP INDEX IF EXISTS idx_pages_source_id;
+      ALTER TABLE pages DROP COLUMN IF EXISTS source_id;
+      DROP TABLE IF EXISTS sources CASCADE;
+      DROP INDEX IF EXISTS idx_links_source;
+      DROP INDEX IF EXISTS idx_links_origin;
+      ALTER TABLE links DROP CONSTRAINT IF EXISTS links_from_to_type_source_origin_unique;
+      ALTER TABLE links DROP COLUMN IF EXISTS link_source;
+      ALTER TABLE links DROP COLUMN IF EXISTS origin_page_id;
+    `);
+
+    // Bootstrap, then schema replay. Either step crashing fails the test.
+    const { PGLITE_SCHEMA_SQL } = await import('../src/core/pglite-schema.ts');
+    await (engine as any).applyForwardReferenceBootstrap();
+    await db.exec(PGLITE_SCHEMA_SQL);
+  } finally {
+    await engine.disconnect();
+  }
+}, 30000);

test/skillpack-install.test.ts

@@ -11,6 +11,7 @@ import {
   mkdtempSync,
   readFileSync,
   rmSync,
+  utimesSync,
   writeFileSync,
 } from 'fs';
 import { dirname, join } from 'path';
@@ -344,6 +345,31 @@ describe('planInstall + applyInstall', () => {
     expect(result.summary.wroteNew).toBeGreaterThan(0);
   });
 
+  it('D-CX-11: --force-unlock works when lock mtime is sub-ms ahead of Date.now (Linux fs jitter)', () => {
+    // Regression guard: on Linux ext4, statSync().mtimeMs has sub-ms precision
+    // while Date.now() is integer ms, so a just-written lock can report a
+    // negative age. If acquireLock does not clamp, stale=false and the
+    // forceUnlock path is unreachable. Simulate deterministically by pushing
+    // the lock's mtime 10ms into the future.
+    const { gbrainRoot } = scratchGbrain();
+    const { workspace, skillsDir } = scratchTarget();
+    const lockFile = join(workspace, '.gbrain-skillpack.lock');
+    writeFileSync(lockFile, '99999');
+    const future = (Date.now() + 10) / 1000;
+    utimesSync(lockFile, future, future);
+    const opts = {
+      gbrainRoot,
+      targetWorkspace: workspace,
+      targetSkillsDir: skillsDir,
+      skillSlug: 'alpha',
+      forceUnlock: true,
+      lockStaleMs: 0,
+    };
+    const plan = planInstall(opts);
+    const result = applyInstall(plan, opts);
+    expect(result.summary.wroteNew).toBeGreaterThan(0);
+  });
+
   it('managed block is written atomically (tmp then rename)', () => {
     const { gbrainRoot } = scratchGbrain();
     const { workspace, skillsDir } = scratchTarget();

test/source-resolver.test.ts

@@ -14,7 +14,7 @@ import { describe, test, expect, beforeEach, afterEach } from 'bun:test';
 import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from 'fs';
 import { join } from 'path';
 import { tmpdir } from 'os';
-import { resolveSourceId, __testing } from '../src/core/source-resolver.ts';
+import { resolveSourceId, getDefaultSourcePath, __testing } from '../src/core/source-resolver.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
 
 // ── Stub engine ────────────────────────────────────────────
@@ -174,6 +174,103 @@ describe('resolveSourceId priority 6 — fallback', () => {
   });
 });
 
+// ── getDefaultSourcePath ───────────────────────────────────
+
+describe('getDefaultSourcePath', () => {
+  function makeStubWithPaths(
+    registeredSources: string[],
+    sourcePaths: Record<string, string | null>,
+    defaultKey: string | null,
+  ): BrainEngine {
+    return {
+      kind: 'pglite',
+      executeRaw: async <T>(sql: string, params?: unknown[]): Promise<T[]> => {
+        if (sql.includes('SELECT id FROM sources WHERE id = $1')) {
+          const target = params?.[0];
+          return (registeredSources.includes(target as string)
+            ? [{ id: target } as unknown as T]
+            : []);
+        }
+        if (sql.includes('SELECT local_path FROM sources WHERE id = $1')) {
+          const target = params?.[0] as string;
+          if (target in sourcePaths) {
+            return [{ local_path: sourcePaths[target] } as unknown as T];
+          }
+          return [];
+        }
+        if (sql.includes('SELECT id, local_path FROM sources')) {
+          return Object.entries(sourcePaths)
+            .filter(([_, p]) => p !== null)
+            .map(([id, local_path]) => ({ id, local_path }) as unknown as T);
+        }
+        return [];
+      },
+      getConfig: async (key: string) => (key === 'sources.default' ? defaultKey : null),
+    } as unknown as BrainEngine;
+  }
+
+  test('returns local_path of resolved default source', async () => {
+    const engine = makeStubWithPaths(['default'], { default: '/path/to/brain' }, null);
+    const path = await getDefaultSourcePath(engine, '/random/dir');
+    expect(path).toBe('/path/to/brain');
+  });
+
+  test('returns null when source has no local_path', async () => {
+    const engine = makeStubWithPaths(['default'], { default: null }, null);
+    const path = await getDefaultSourcePath(engine, '/random/dir');
+    expect(path).toBeNull();
+  });
+
+  test('throws on DB error (does not silently swallow)', async () => {
+    const engine = {
+      kind: 'pglite',
+      executeRaw: async () => {
+        throw new Error('connection refused');
+      },
+      getConfig: async () => null,
+    } as unknown as BrainEngine;
+    await expect(getDefaultSourcePath(engine, '/random/dir')).rejects.toThrow(/connection refused/);
+  });
+
+  test('falls back to legacy sync.repo_path config when sources.local_path is null', async () => {
+    // Pre-v0.18 brains: 'default' source exists but local_path is NULL; the
+    // repo path lives in the global config table under sync.repo_path.
+    const engine = {
+      kind: 'pglite',
+      executeRaw: async <T>(sql: string, params?: unknown[]): Promise<T[]> => {
+        if (sql.includes('SELECT id FROM sources WHERE id = $1')) {
+          return [{ id: params?.[0] } as unknown as T];
+        }
+        if (sql.includes('SELECT local_path FROM sources WHERE id = $1')) {
+          return [{ local_path: null } as unknown as T];
+        }
+        if (sql.includes('SELECT id, local_path FROM sources')) {
+          return [];
+        }
+        return [];
+      },
+      getConfig: async (key: string) => {
+        if (key === 'sources.default') return null;
+        if (key === 'sync.repo_path') return '/legacy/brain/path';
+        return null;
+      },
+    } as unknown as BrainEngine;
+    const path = await getDefaultSourcePath(engine, '/random/dir');
+    expect(path).toBe('/legacy/brain/path');
+  });
+
+  test('respects source resolution chain (registered local_path wins over default)', async () => {
+    // CWD is inside /custom/path → wiki source matches by path → wiki's local_path returned.
+    const engine = makeStubWithPaths(
+      ['default', 'wiki'],
+      { default: '/default/path', wiki: '/custom/path' },
+      'default',
+    );
+    const path = await getDefaultSourcePath(engine, '/custom/path/sub');
+    expect(path).toBe('/custom/path');
+  });
+});
+
 // ── Regex validation ───────────────────────────────────────
 
 describe('SOURCE_ID_RE', () => {

test/storage-config.test.ts

@@ -0,0 +1,336 @@
+import { test, expect, describe, beforeEach } from 'bun:test';
+import { mkdtempSync, rmSync, writeFileSync, mkdirSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import {
+  validateStorageConfig,
+  isGitTracked,
+  isSupabaseOnly,
+  getStorageTier,
+  loadStorageConfig,
+  normalizeAndValidateStorageConfig,
+  StorageConfigError,
+  __resetMissingStorageWarning,
+} from '../src/core/storage-config.ts';
+import type { StorageConfig } from '../src/core/storage-config.ts';
+
+describe('Storage Configuration', () => {
+  const testConfig: StorageConfig = {
+    db_tracked: ['people/', 'companies/', 'deals/'],
+    db_only: ['media/x/', 'media/articles/', 'meetings/transcripts/'],
+  };
+
+  describe('validateStorageConfig', () => {
+    test('should return no warnings for valid config', () => {
+      const warnings = validateStorageConfig(testConfig);
+      expect(warnings).toEqual([]);
+    });
+
+    test('should warn about overlap between db_tracked and db_only', () => {
+      const invalidConfig: StorageConfig = {
+        db_tracked: ['people/', 'media/'],
+        db_only: ['media/', 'articles/'],
+      };
+      const warnings = validateStorageConfig(invalidConfig);
+      expect(warnings).toContain('Directory "media/" appears in both db_tracked and db_only');
+    });
+
+    test('should warn about paths not ending with /', () => {
+      const invalidConfig: StorageConfig = {
+        db_tracked: ['people', 'companies/'],
+        db_only: ['media/x/', 'articles'],
+      };
+      const warnings = validateStorageConfig(invalidConfig);
+      expect(warnings).toContain('Directory path "people" should end with "/" for consistency');
+      expect(warnings).toContain('Directory path "articles" should end with "/" for consistency');
+    });
+  });
+
+  describe('Storage tier detection', () => {
+    test('identifies db-tracked pages', () => {
+      expect(isGitTracked('people/john-doe', testConfig)).toBe(true);
+      expect(isGitTracked('companies/acme-corp', testConfig)).toBe(true);
+      expect(isGitTracked('deals/series-a', testConfig)).toBe(true);
+    });
+
+    test('identifies db-only pages', () => {
+      expect(isSupabaseOnly('media/x/tweet-123', testConfig)).toBe(true);
+      expect(isSupabaseOnly('media/articles/blog-post', testConfig)).toBe(true);
+      expect(isSupabaseOnly('meetings/transcripts/standup', testConfig)).toBe(true);
+    });
+
+    test('returns false for non-matching paths', () => {
+      expect(isGitTracked('media/x/tweet-123', testConfig)).toBe(false);
+      expect(isSupabaseOnly('people/john-doe', testConfig)).toBe(false);
+    });
+
+    test('correctly determines storage tier (canonical names)', () => {
+      expect(getStorageTier('people/john-doe', testConfig)).toBe('db_tracked');
+      expect(getStorageTier('media/x/tweet-123', testConfig)).toBe('db_only');
+      expect(getStorageTier('projects/random-thing', testConfig)).toBe('unspecified');
+    });
+
+    test('handles prefix edge cases', () => {
+      expect(isGitTracked('people', testConfig)).toBe(false);
+      expect(isGitTracked('people/', testConfig)).toBe(true);
+      expect(isGitTracked('peoplex/test', testConfig)).toBe(false);
+      expect(isSupabaseOnly('mediax/test', testConfig)).toBe(false);
+    });
+
+    test('normalizeAndValidateStorageConfig auto-adds trailing slash silently with info note', () => {
+      __resetMissingStorageWarning();
+      const warnings: string[] = [];
+      const orig = console.warn;
+      console.warn = (...a: unknown[]) => { warnings.push(a.map(String).join(' ')); };
+      try {
+        const out = normalizeAndValidateStorageConfig({
+          db_tracked: ['people', 'companies/'],
+          db_only: ['media/x'],
+        });
+        expect(out.db_tracked).toEqual(['people/', 'companies/']);
+        expect(out.db_only).toEqual(['media/x/']);
+        expect(warnings.length).toBe(1);
+        expect(warnings[0]).toMatch(/normalized.*"people".*"people\/".*"media\/x".*"media\/x\/"/);
+      } finally {
+        console.warn = orig;
+      }
+    });
+
+    test('normalizeAndValidateStorageConfig throws on tier overlap', () => {
+      __resetMissingStorageWarning();
+      expect(() =>
+        normalizeAndValidateStorageConfig({
+          db_tracked: ['media/'],
+          db_only: ['media/'],
+        }),
+      ).toThrow(StorageConfigError);
+    });
+
+    test('regression — media/xerox does NOT match media/x (path-segment matcher)', () => {
+      // Without path-segment matching, slug.startsWith('media/x') would falsely
+      // match 'media/xerox/foo'. The new matcher requires trailing '/'; if the
+      // user's config has 'media/x' (no slash), the matcher refuses to match —
+      // the validator's auto-normalize (step 7) ensures canonical input.
+      const collisionConfig: StorageConfig = {
+        db_tracked: [],
+        db_only: ['media/x/'], // canonical, with trailing slash
+      };
+      expect(isSupabaseOnly('media/xerox/something', collisionConfig)).toBe(false);
+      expect(isSupabaseOnly('media/x/tweet-1', collisionConfig)).toBe(true);
+
+      // Non-canonical input (no trailing slash) is refused by the matcher.
+      const noSlashConfig: StorageConfig = {
+        db_tracked: [],
+        db_only: ['media/x'],
+      };
+      expect(isSupabaseOnly('media/xerox/foo', noSlashConfig)).toBe(false);
+      expect(isSupabaseOnly('media/x/tweet-1', noSlashConfig)).toBe(false);
+    });
+  });
+});
+
+describe('loadStorageConfig — real-disk loader', () => {
+  let tmp: string;
+  let originalWarn: typeof console.warn;
+  let warnings: string[];
+
+  beforeEach(() => {
+    tmp = mkdtempSync(join(tmpdir(), 'gbrain-storage-test-'));
+    __resetMissingStorageWarning();
+    warnings = [];
+    originalWarn = console.warn;
+    console.warn = (...args: unknown[]) => {
+      warnings.push(args.map(String).join(' '));
+    };
+  });
+
+  function cleanup(): void {
+    console.warn = originalWarn;
+    rmSync(tmp, { recursive: true, force: true });
+  }
+
+  test('returns null when repoPath is missing', () => {
+    try {
+      expect(loadStorageConfig(undefined)).toBeNull();
+      expect(loadStorageConfig(null)).toBeNull();
+      expect(loadStorageConfig('')).toBeNull();
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('returns null when gbrain.yml does not exist', () => {
+    try {
+      expect(loadStorageConfig(tmp)).toBeNull();
+      expect(warnings).toEqual([]);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('loads canonical gbrain.yml — the test that would have caught the original gray-matter P0', () => {
+    try {
+      const yaml = `# Brain storage tiering config
+storage:
+  db_tracked:
+    - people/
+    - companies/
+    - deals/
+  db_only:
+    - media/x/
+    - media/articles/
+`;
+      writeFileSync(join(tmp, 'gbrain.yml'), yaml);
+      const config = loadStorageConfig(tmp);
+      expect(config).not.toBeNull();
+      expect(config!.db_tracked).toEqual(['people/', 'companies/', 'deals/']);
+      expect(config!.db_only).toEqual(['media/x/', 'media/articles/']);
+      expect(warnings).toEqual([]);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('handles inline comments and blank lines', () => {
+    try {
+      const yaml = `
+storage:
+  db_tracked:
+    - people/  # human-curated
+    - companies/
+
+  db_only:
+    - media/x/    # bulk tweets
+`;
+      writeFileSync(join(tmp, 'gbrain.yml'), yaml);
+      const config = loadStorageConfig(tmp);
+      expect(config!.db_tracked).toEqual(['people/', 'companies/']);
+      expect(config!.db_only).toEqual(['media/x/']);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('strips quoted values', () => {
+    try {
+      const yaml = `storage:
+  db_tracked:
+    - "people/"
+    - 'companies/'
+  db_only: []
+`;
+      writeFileSync(join(tmp, 'gbrain.yml'), yaml);
+      const config = loadStorageConfig(tmp);
+      expect(config!.db_tracked).toEqual(['people/', 'companies/']);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('reads deprecated keys (git_tracked / supabase_only) with once-per-process warning', () => {
+    try {
+      const yaml = `storage:
+  git_tracked:
+    - people/
+  supabase_only:
+    - media/x/
+`;
+      writeFileSync(join(tmp, 'gbrain.yml'), yaml);
+      const config = loadStorageConfig(tmp);
+      expect(config!.db_tracked).toEqual(['people/']);
+      expect(config!.db_only).toEqual(['media/x/']);
+      expect(warnings.some((w) => /deprecated/.test(w))).toBe(true);
+
+      // Second call: no second deprecation warning (once-per-process).
+      const before = warnings.length;
+      loadStorageConfig(tmp);
+      const newWarnings = warnings.slice(before);
+      expect(newWarnings.filter((w) => /deprecated/.test(w))).toEqual([]);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('canonical keys win over deprecated keys when both present', () => {
+    try {
+      const yaml = `storage:
+  db_tracked:
+    - new-people/
+  git_tracked:
+    - old-people/
+  db_only:
+    - new-media/
+  supabase_only:
+    - old-media/
+`;
+      writeFileSync(join(tmp, 'gbrain.yml'), yaml);
+      const config = loadStorageConfig(tmp);
+      expect(config!.db_tracked).toEqual(['new-people/']);
+      expect(config!.db_only).toEqual(['new-media/']);
+      // Stronger deprecation warning when both shapes coexist.
+      expect(warnings.some((w) => /deprecated.*ignored/.test(w))).toBe(true);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('warns once when gbrain.yml exists but storage section is missing', () => {
+    try {
+      writeFileSync(join(tmp, 'gbrain.yml'), 'something_else: foo\n');
+      const config = loadStorageConfig(tmp);
+      expect(config).toBeNull();
+      expect(warnings.length).toBe(1);
+      expect(warnings[0]).toMatch(/no storage configuration/);
+
+      // Second call: no additional warning (once-per-process).
+      loadStorageConfig(tmp);
+      expect(warnings.length).toBe(1);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('warns when storage section is empty', () => {
+    try {
+      const yaml = `storage:
+  db_tracked: []
+  db_only: []
+`;
+      writeFileSync(join(tmp, 'gbrain.yml'), yaml);
+      const config = loadStorageConfig(tmp);
+      // Empty config is returned (not null) but warning fires.
+      expect(config).not.toBeNull();
+      expect(config!.db_tracked).toEqual([]);
+      expect(config!.db_only).toEqual([]);
+      const noConfigWarnings = warnings.filter((w) => /no storage configuration/.test(w));
+      expect(noConfigWarnings.length).toBe(1);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('throws on unreadable gbrain.yml (permission denied) — does not silently disable feature', () => {
+    try {
+      const yamlPath = join(tmp, 'gbrain.yml');
+      writeFileSync(yamlPath, 'storage:\n  db_tracked:\n    - x/\n');
+      // Simulate unreadable: chmod 000. May not work on all CI; skip if not supported.
+      const fs = require('fs');
+      fs.chmodSync(yamlPath, 0o000);
+      try {
+        // On systems where chmod 000 actually denies read, this throws.
+        // On systems where root can still read (CI containers), the read succeeds
+        // and the test is a no-op assertion.
+        try {
+          fs.readFileSync(yamlPath, 'utf-8');
+          // Read succeeded — skip strict assertion.
+        } catch {
+          expect(() => loadStorageConfig(tmp)).toThrow();
+        }
+      } finally {
+        fs.chmodSync(yamlPath, 0o644);
+      }
+    } finally {
+      cleanup();
+    }
+  });
+});

test/storage-export.test.ts

@@ -0,0 +1,146 @@
+/**
+ * Tests for export.ts --restore-only resolution chain — step 9 of v0.22.3.
+ *
+ * D5: --repo → sources.getDefault() → hard error. Never fall through to
+ * cwd. Issue #9: bare try/catch removed from storage.ts:37.
+ *
+ * Tests use PGLite in-memory and a captured-output approach (process.exit
+ * is intercepted) to verify the resolution chain produces the right
+ * repoPath OR the right error.
+ */
+
+import { describe, test, expect, beforeEach, afterEach, beforeAll, afterAll } from 'bun:test';
+import { mkdtempSync, rmSync, writeFileSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { runExport } from '../src/commands/export.ts';
+import { __resetMissingStorageWarning } from '../src/core/storage-config.ts';
+
+let engine: PGLiteEngine;
+let tmp: string;
+let outDir: string;
+let exitCode: number | null;
+let originalExit: typeof process.exit;
+let originalErr: typeof console.error;
+let originalLog: typeof console.log;
+let stderr: string[];
+let stdout: string[];
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+});
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+beforeEach(async () => {
+  tmp = mkdtempSync(join(tmpdir(), 'gbrain-export-test-'));
+  outDir = join(tmp, 'out');
+  exitCode = null;
+  stderr = [];
+  stdout = [];
+  __resetMissingStorageWarning();
+
+  originalExit = process.exit;
+  process.exit = ((code?: number) => {
+    exitCode = code ?? 0;
+    throw new Error(`__test_exit__:${code}`);
+  }) as typeof process.exit;
+
+  originalErr = console.error;
+  console.error = (...args: unknown[]) => {
+    stderr.push(args.map(String).join(' '));
+  };
+
+  originalLog = console.log;
+  console.log = (...args: unknown[]) => {
+    stdout.push(args.map(String).join(' '));
+  };
+
+  // Reset DB state between tests
+  const tables = ['content_chunks', 'links', 'tags', 'raw_data', 'timeline_entries', 'page_versions', 'ingest_log', 'pages', 'sources'];
+  for (const t of tables) {
+    await (engine as unknown as { db: { exec(sql: string): Promise<unknown> } }).db.exec(`DELETE FROM ${t}`);
+  }
+  // Recreate the default source (the schema seed but truncated above).
+  await engine.executeRaw(
+    `INSERT INTO sources (id, name) VALUES ('default', 'Default') ON CONFLICT DO NOTHING`,
+  );
+});
+
+afterEach(() => {
+  process.exit = originalExit;
+  console.error = originalErr;
+  console.log = originalLog;
+  rmSync(tmp, { recursive: true, force: true });
+});
+
+async function tryRunExport(args: string[]): Promise<void> {
+  try {
+    await runExport(engine, args);
+  } catch (e) {
+    // Swallow only the test-exit sentinel; rethrow others for visibility.
+    if (!(e instanceof Error && e.message.startsWith('__test_exit__:'))) {
+      throw e;
+    }
+  }
+}
+
+describe('export --restore-only resolution chain (D5)', () => {
+  test('hard-errors when --restore-only has no --repo and no default source path', async () => {
+    // sources.default has no local_path (the seeded shape).
+    await tryRunExport(['--dir', outDir, '--restore-only']);
+    expect(exitCode).toBe(1);
+    expect(stderr.join('\n')).toMatch(/requires --repo|configured default source/);
+  });
+
+  test('uses explicit --repo when provided', async () => {
+    // Make a brain repo with gbrain.yml that has empty db_only — so we
+    // exit through the "0 pages to restore" path without needing real data.
+    writeFileSync(
+      join(tmp, 'gbrain.yml'),
+      `storage:
+  db_tracked: []
+  db_only: []
+`,
+    );
+    await tryRunExport(['--dir', outDir, '--restore-only', '--repo', tmp]);
+    expect(exitCode).toBeNull(); // no exit
+    expect(stdout.some((line) => line.includes('Restoring 0'))).toBe(true);
+  });
+
+  test('falls back to sources default local_path when --repo absent', async () => {
+    // Configure default source path, write a real gbrain.yml so the storage
+    // config check passes — without gbrain.yml the Codex-P0 guard correctly
+    // refuses --restore-only (no storage config to scope to).
+    await engine.executeRaw(`UPDATE sources SET local_path = $1 WHERE id = 'default'`, [tmp]);
+    writeFileSync(
+      join(tmp, 'gbrain.yml'),
+      `storage:\n  db_tracked: []\n  db_only:\n    - media/x/\n`,
+    );
+    await tryRunExport(['--dir', outDir, '--restore-only']);
+    expect(exitCode).toBeNull(); // resolution succeeded
+  });
+
+  test('refuses --restore-only when no storage config is present (Codex P0)', async () => {
+    // Default source has a path but no gbrain.yml. Without a storage config,
+    // --restore-only would silently fall through to a full export — exactly
+    // the silent-footgun D5 was supposed to prevent.
+    await engine.executeRaw(`UPDATE sources SET local_path = $1 WHERE id = 'default'`, [tmp]);
+    await tryRunExport(['--dir', outDir, '--restore-only']);
+    expect(exitCode).toBe(1);
+    expect(stderr.join('\n')).toMatch(/storage tiering config|gbrain\.yml/);
+  });
+
+  test('non-restore export does NOT require --repo (D26)', async () => {
+    // Regular export works without --repo since it dumps everything from DB.
+    // Pages table is empty → exports 0 pages, no error.
+    await tryRunExport(['--dir', outDir]);
+    expect(exitCode).toBeNull();
+    expect(stdout.some((line) => line.includes('Exporting 0'))).toBe(true);
+  });
+});

test/storage-pglite.test.ts

@@ -0,0 +1,171 @@
+/**
+ * PGLite lifecycle test for storage tiering — D8 + D4 of v0.22.3.
+ *
+ * Per the plan: "the full PGLite lifecycle for D8's both-engines requirement.
+ * gbrain.yml load → gbrain storage status → soft-warn message present →
+ * manageGitignore happy-path on a tmp dir. PGLite-specific path for the
+ * slugPrefix filter."
+ *
+ * In-memory PGLite, no Docker, no DATABASE_URL. Runs instantly in CI.
+ */
+
+import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
+import { mkdtempSync, rmSync, writeFileSync, readFileSync, existsSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import {
+  getStorageStatus,
+  formatStorageStatusHuman,
+  __resetPGLiteWarn,
+} from '../src/commands/storage.ts';
+import { manageGitignore, __resetPGLiteTierWarn } from '../src/commands/sync.ts';
+import { __resetMissingStorageWarning } from '../src/core/storage-config.ts';
+
+let engine: PGLiteEngine;
+let tmp: string;
+let warnings: string[];
+let originalWarn: typeof console.warn;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+});
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+beforeEach(async () => {
+  tmp = mkdtempSync(join(tmpdir(), 'gbrain-pglite-test-'));
+  __resetMissingStorageWarning();
+  __resetPGLiteWarn();
+  __resetPGLiteTierWarn();
+  warnings = [];
+  originalWarn = console.warn;
+  console.warn = (...args: unknown[]) => {
+    warnings.push(args.map(String).join(' '));
+  };
+
+  // Reset DB between tests.
+  const tables = ['content_chunks', 'links', 'tags', 'raw_data', 'timeline_entries', 'page_versions', 'ingest_log', 'pages', 'sources'];
+  for (const t of tables) {
+    await (engine as unknown as { db: { exec(sql: string): Promise<unknown> } }).db.exec(`DELETE FROM ${t}`);
+  }
+  await engine.executeRaw(
+    `INSERT INTO sources (id, name) VALUES ('default', 'Default') ON CONFLICT DO NOTHING`,
+  );
+});
+
+function cleanup(): void {
+  console.warn = originalWarn;
+  rmSync(tmp, { recursive: true, force: true });
+}
+
+function writeGbrainYml(): void {
+  writeFileSync(
+    join(tmp, 'gbrain.yml'),
+    `storage:
+  db_tracked:
+    - people/
+  db_only:
+    - media/x/
+`,
+  );
+}
+
+describe('Storage tiering on PGLite — full lifecycle (D8 + D4)', () => {
+  test('engine.kind is pglite', () => {
+    try {
+      expect(engine.kind).toBe('pglite');
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('getStorageStatus loads gbrain.yml and reports tier counts', async () => {
+    try {
+      writeGbrainYml();
+      await engine.putPage('people/alice', { type: 'person', title: 'Alice', compiled_truth: '', timeline: '' });
+      await engine.putPage('media/x/tweet-1', { type: 'concept', title: 'Tweet', compiled_truth: '', timeline: '' });
+      await engine.putPage('media/x/tweet-2', { type: 'concept', title: 'Tweet 2', compiled_truth: '', timeline: '' });
+      await engine.putPage('random/note', { type: 'concept', title: 'Random', compiled_truth: '', timeline: '' });
+
+      const result = await getStorageStatus(engine, tmp);
+      expect(result.totalPages).toBe(4);
+      expect(result.pagesByTier.db_tracked).toBe(1);
+      expect(result.pagesByTier.db_only).toBe(2);
+      expect(result.pagesByTier.unspecified).toBe(1);
+      expect(result.config!.db_only).toEqual(['media/x/']);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('manageGitignore on PGLite emits the D4 soft-warn (once per process)', () => {
+    try {
+      writeGbrainYml();
+      manageGitignore(tmp, 'pglite');
+      expect(warnings.some((w) => /limited effect on PGLite/.test(w))).toBe(true);
+      expect(existsSync(join(tmp, '.gitignore'))).toBe(true);
+      expect(readFileSync(join(tmp, '.gitignore'), 'utf-8')).toContain('media/x/');
+
+      // Second call: no second warning (once-per-process).
+      const before = warnings.length;
+      manageGitignore(tmp, 'pglite');
+      const newWarnings = warnings.slice(before).filter((w) => /limited effect on PGLite/.test(w));
+      expect(newWarnings).toEqual([]);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('manageGitignore on Postgres does NOT emit the PGLite warning', () => {
+    try {
+      writeGbrainYml();
+      manageGitignore(tmp, 'postgres');
+      expect(warnings.filter((w) => /limited effect on PGLite/.test(w))).toEqual([]);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('slugPrefix engine filter works on PGLite (Issue #13)', async () => {
+    try {
+      await engine.putPage('media/x/tweet-1', { type: 'concept', title: 'T1', compiled_truth: '', timeline: '' });
+      await engine.putPage('media/x/tweet-2', { type: 'concept', title: 'T2', compiled_truth: '', timeline: '' });
+      await engine.putPage('media/articles/post-1', { type: 'concept', title: 'A1', compiled_truth: '', timeline: '' });
+
+      const xOnly = await engine.listPages({ slugPrefix: 'media/x/', limit: 100 });
+      expect(xOnly.map((p) => p.slug).sort()).toEqual(['media/x/tweet-1', 'media/x/tweet-2']);
+    } finally {
+      cleanup();
+    }
+  });
+
+  test('end-to-end: gbrain.yml + putPage + storage status + .gitignore', async () => {
+    try {
+      writeGbrainYml();
+      await engine.putPage('people/alice', { type: 'person', title: 'Alice', compiled_truth: '', timeline: '' });
+      await engine.putPage('media/x/tweet-1', { type: 'concept', title: 'T1', compiled_truth: '', timeline: '' });
+
+      // Status reads tier counts correctly.
+      const status = await getStorageStatus(engine, tmp);
+      expect(status.config).not.toBeNull();
+      expect(status.pagesByTier.db_only).toBe(1);
+
+      // Render to human output without errors.
+      const out = formatStorageStatusHuman(status);
+      expect(out).toContain('DB only:        1 pages');
+
+      // .gitignore management produces a managed block.
+      manageGitignore(tmp, 'pglite');
+      const gitignore = readFileSync(join(tmp, '.gitignore'), 'utf-8');
+      expect(gitignore).toContain('# Auto-managed by gbrain');
+      expect(gitignore).toContain('media/x/');
+    } finally {
+      cleanup();
+    }
+  });
+});

test/storage-status.test.ts

@@ -0,0 +1,111 @@
+/**
+ * Tests for storage-status formatters — step 10 of v0.22.3.
+ *
+ * Issue #10 + D14: split storage.ts into pure data + JSON formatter +
+ * human formatter (matching orphans.ts). Formatters are now pure
+ * functions; this test file pins their output contracts.
+ */
+
+import { describe, test, expect } from 'bun:test';
+import {
+  formatStorageStatusJson,
+  formatStorageStatusHuman,
+  type StorageStatusResult,
+} from '../src/commands/storage.ts';
+
+const baseResult: StorageStatusResult = {
+  config: {
+    db_tracked: ['people/', 'companies/'],
+    db_only: ['media/x/', 'media/articles/'],
+  },
+  repoPath: '/data/brain',
+  totalPages: 12500,
+  pagesByTier: { db_tracked: 2156, db_only: 10100, unspecified: 244 },
+  missingFiles: [],
+  diskUsageByTier: { db_tracked: 45_200_000, db_only: 2_100_000_000, unspecified: 0 },
+  warnings: [],
+};
+
+describe('formatStorageStatusJson', () => {
+  test('produces parseable JSON of the StorageStatusResult shape', () => {
+    const out = formatStorageStatusJson(baseResult);
+    const parsed = JSON.parse(out);
+    expect(parsed.repoPath).toBe('/data/brain');
+    expect(parsed.totalPages).toBe(12500);
+    expect(parsed.pagesByTier.db_only).toBe(10100);
+    expect(parsed.config.db_tracked).toEqual(['people/', 'companies/']);
+  });
+
+  test('handles null config (no gbrain.yml present)', () => {
+    const out = formatStorageStatusJson({ ...baseResult, config: null, totalPages: 5 });
+    const parsed = JSON.parse(out);
+    expect(parsed.config).toBeNull();
+    expect(parsed.totalPages).toBe(5);
+  });
+});
+
+describe('formatStorageStatusHuman', () => {
+  test('shows tier counts and disk usage when config present', () => {
+    const out = formatStorageStatusHuman(baseResult);
+    expect(out).toContain('Storage Status');
+    expect(out).toContain('Repository: /data/brain');
+    expect(out).toContain('Total pages: 12500');
+    expect(out).toContain('DB tracked:     2,156 pages');
+    expect(out).toContain('DB only:        10,100 pages');
+    expect(out).toContain('Unspecified:    244 pages');
+  });
+
+  test('shows ASCII separators only — no unicode (D10)', () => {
+    const out = formatStorageStatusHuman(baseResult);
+    expect(out).not.toContain('─'); // U+2500 box drawing
+    expect(out).not.toContain('•'); // U+2022 bullet
+    expect(out).toContain('-------------'); // ASCII fallback
+  });
+
+  test('shows fallback message when config is null', () => {
+    const out = formatStorageStatusHuman({ ...baseResult, config: null });
+    expect(out).toContain('No gbrain.yml configuration found.');
+    expect(out).toContain('All pages are stored in git by default.');
+  });
+
+  test('shows missing-files block when list is non-empty, capped at 10', () => {
+    const missing = Array.from({ length: 25 }, (_, i) => ({
+      slug: `media/x/tweet-${i}`,
+      expectedPath: `/data/brain/media/x/tweet-${i}.md`,
+    }));
+    const out = formatStorageStatusHuman({ ...baseResult, missingFiles: missing });
+    expect(out).toContain('Missing Files (need restore):');
+    expect(out).toContain('media/x/tweet-0');
+    expect(out).toContain('media/x/tweet-9'); // 10th
+    expect(out).not.toContain('media/x/tweet-10'); // 11th truncated
+    expect(out).toContain('and 15 more');
+    expect(out).toContain('gbrain export --restore-only --repo "/data/brain"');
+  });
+
+  test('shows configuration listing for both tiers', () => {
+    const out = formatStorageStatusHuman(baseResult);
+    expect(out).toContain('DB tracked directories:');
+    expect(out).toContain('  - people/');
+    expect(out).toContain('  - companies/');
+    expect(out).toContain('DB-only directories:');
+    expect(out).toContain('  - media/x/');
+    expect(out).toContain('  - media/articles/');
+  });
+
+  test('shows warnings inline when present', () => {
+    const out = formatStorageStatusHuman({
+      ...baseResult,
+      warnings: ['Directory path "people" should end with "/" for consistency'],
+    });
+    expect(out).toContain('Warnings:');
+    expect(out).toContain('! Directory path "people"');
+  });
+
+  test('omits disk-usage block when both tiers report 0 bytes', () => {
+    const out = formatStorageStatusHuman({
+      ...baseResult,
+      diskUsageByTier: { db_tracked: 0, db_only: 0, unspecified: 0 },
+    });
+    expect(out).not.toContain('Disk Usage:');
+  });
+});

test/storage-sync.test.ts

@@ -0,0 +1,144 @@
+/**
+ * Tests for sync.ts manageGitignore() — step 8 of v0.22.3 storage tiering.
+ *
+ * Issue #2: function was defined but never invoked. Now wired into runSync
+ * after a successful sync (skips on dry_run / blocked_by_failures / failure).
+ *
+ * Tests cover: happy path, idempotency, GBRAIN_NO_GITIGNORE escape hatch,
+ * submodule detection, write-error graceful degradation, and the "no
+ * config — no-op" path.
+ */
+
+import { describe, test, expect, beforeEach, afterEach } from 'bun:test';
+import { mkdtempSync, mkdirSync, rmSync, writeFileSync, readFileSync, existsSync, chmodSync, symlinkSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { manageGitignore } from '../src/commands/sync.ts';
+import { __resetMissingStorageWarning } from '../src/core/storage-config.ts';
+
+let tmp: string;
+let warnings: string[];
+let originalWarn: typeof console.warn;
+let originalEnv: string | undefined;
+
+beforeEach(() => {
+  tmp = mkdtempSync(join(tmpdir(), 'gbrain-mgi-test-'));
+  __resetMissingStorageWarning();
+  warnings = [];
+  originalWarn = console.warn;
+  console.warn = (...args: unknown[]) => {
+    warnings.push(args.map(String).join(' '));
+  };
+  originalEnv = process.env.GBRAIN_NO_GITIGNORE;
+  delete process.env.GBRAIN_NO_GITIGNORE;
+});
+
+afterEach(() => {
+  console.warn = originalWarn;
+  if (originalEnv === undefined) delete process.env.GBRAIN_NO_GITIGNORE;
+  else process.env.GBRAIN_NO_GITIGNORE = originalEnv;
+  // Restore permissions for cleanup.
+  try {
+    chmodSync(tmp, 0o755);
+  } catch {
+    /* ignore */
+  }
+  rmSync(tmp, { recursive: true, force: true });
+});
+
+function writeStorageConfig(): void {
+  writeFileSync(
+    join(tmp, 'gbrain.yml'),
+    `storage:
+  db_tracked:
+    - people/
+  db_only:
+    - media/x/
+    - media/articles/
+`,
+  );
+}
+
+describe('manageGitignore', () => {
+  test('no-op when gbrain.yml is absent', () => {
+    manageGitignore(tmp);
+    expect(existsSync(join(tmp, '.gitignore'))).toBe(false);
+    expect(warnings).toEqual([]);
+  });
+
+  test('no-op when storage config has empty db_only', () => {
+    writeFileSync(
+      join(tmp, 'gbrain.yml'),
+      `storage:
+  db_tracked:
+    - people/
+  db_only: []
+`,
+    );
+    manageGitignore(tmp);
+    expect(existsSync(join(tmp, '.gitignore'))).toBe(false);
+  });
+
+  test('appends db_only directories to .gitignore — happy path', () => {
+    writeStorageConfig();
+    manageGitignore(tmp);
+    const content = readFileSync(join(tmp, '.gitignore'), 'utf-8');
+    expect(content).toContain('# Auto-managed by gbrain');
+    expect(content).toContain('media/x/');
+    expect(content).toContain('media/articles/');
+  });
+
+  test('idempotent — running twice does NOT duplicate entries', () => {
+    writeStorageConfig();
+    manageGitignore(tmp);
+    manageGitignore(tmp);
+    const content = readFileSync(join(tmp, '.gitignore'), 'utf-8');
+    const xCount = (content.match(/^media\/x\/$/gm) || []).length;
+    const articlesCount = (content.match(/^media\/articles\/$/gm) || []).length;
+    expect(xCount).toBe(1);
+    expect(articlesCount).toBe(1);
+  });
+
+  test('preserves user-written .gitignore entries', () => {
+    writeStorageConfig();
+    writeFileSync(join(tmp, '.gitignore'), '# my own rules\n*.swp\nnode_modules/\n');
+    manageGitignore(tmp);
+    const content = readFileSync(join(tmp, '.gitignore'), 'utf-8');
+    expect(content).toContain('# my own rules');
+    expect(content).toContain('*.swp');
+    expect(content).toContain('node_modules/');
+    expect(content).toContain('media/x/');
+  });
+
+  test('GBRAIN_NO_GITIGNORE=1 skips entirely', () => {
+    writeStorageConfig();
+    process.env.GBRAIN_NO_GITIGNORE = '1';
+    manageGitignore(tmp);
+    expect(existsSync(join(tmp, '.gitignore'))).toBe(false);
+  });
+
+  test('skips with actionable warning when repo is a git submodule', () => {
+    writeStorageConfig();
+    // Submodule: .git is a file containing `gitdir: ...` instead of a directory.
+    writeFileSync(join(tmp, '.git'), 'gitdir: ../.git/modules/sub\n');
+    manageGitignore(tmp);
+    expect(existsSync(join(tmp, '.gitignore'))).toBe(false);
+    expect(warnings.some((w) => /submodule/.test(w))).toBe(true);
+  });
+
+  test('proceeds when .git is a directory (regular repo)', () => {
+    writeStorageConfig();
+    mkdirSync(join(tmp, '.git'));
+    manageGitignore(tmp);
+    expect(existsSync(join(tmp, '.gitignore'))).toBe(true);
+    expect(warnings.filter((w) => /submodule/.test(w))).toEqual([]);
+  });
+
+  test('warns and skips when .gitignore write fails (read-only filesystem simulation)', () => {
+    writeStorageConfig();
+    // Create a .gitignore as a directory — write to that path will fail with EISDIR.
+    mkdirSync(join(tmp, '.gitignore'));
+    manageGitignore(tmp);
+    expect(warnings.some((w) => /Could not (read|update)/.test(w))).toBe(true);
+  });
+});

test/sync-concurrency.test.ts

@@ -0,0 +1,123 @@
+/**
+ * Unit tests for the shared concurrency-policy helper. Covers:
+ *
+ *   - Q5: autoConcurrency() returns correct counts for PGLite, explicit
+ *     override, auto path above/below threshold.
+ *   - Q1: shouldRunParallel() respects explicit opt-in even on small diffs.
+ *   - Q2/T3: parseWorkers() throws on bad CLI input (0, -3, "foo", "1.5").
+ *
+ * These exist because the prior policy was duplicated across three call sites
+ * (performSync, performFullSync, jobs handler) with subtle differences.
+ * Centralized helper + tests prevents the next drift.
+ */
+import { describe, expect, test } from 'bun:test';
+import {
+  autoConcurrency,
+  shouldRunParallel,
+  parseWorkers,
+  AUTO_CONCURRENCY_FILE_THRESHOLD,
+  PARALLEL_FILE_FLOOR,
+  DEFAULT_PARALLEL_WORKERS,
+} from '../src/core/sync-concurrency.ts';
+import type { BrainEngine } from '../src/core/engine.ts';
+
+// Minimal engine stub — autoConcurrency only reads .kind.
+function engineOfKind(kind: 'postgres' | 'pglite'): BrainEngine {
+  return { kind } as unknown as BrainEngine;
+}
+
+describe('autoConcurrency', () => {
+  test('PGLite always serial (single connection)', () => {
+    expect(autoConcurrency(engineOfKind('pglite'), 1000)).toBe(1);
+    expect(autoConcurrency(engineOfKind('pglite'), 1000, 8)).toBe(1);
+    expect(autoConcurrency(engineOfKind('pglite'), 0)).toBe(1);
+  });
+
+  test('Postgres + explicit override wins', () => {
+    expect(autoConcurrency(engineOfKind('postgres'), 5, 4)).toBe(4);
+    expect(autoConcurrency(engineOfKind('postgres'), 5, 1)).toBe(1);
+    expect(autoConcurrency(engineOfKind('postgres'), 5, 16)).toBe(16);
+  });
+
+  test('Postgres explicit 0 clamped to 1 (paranoia — parseWorkers should reject first)', () => {
+    expect(autoConcurrency(engineOfKind('postgres'), 100, 0)).toBe(1);
+    expect(autoConcurrency(engineOfKind('postgres'), 100, -5)).toBe(1);
+  });
+
+  test('Postgres + auto path: under threshold serial', () => {
+    expect(autoConcurrency(engineOfKind('postgres'), 50)).toBe(1);
+    expect(autoConcurrency(engineOfKind('postgres'), AUTO_CONCURRENCY_FILE_THRESHOLD)).toBe(1);
+  });
+
+  test('Postgres + auto path: above threshold parallel', () => {
+    expect(autoConcurrency(engineOfKind('postgres'), AUTO_CONCURRENCY_FILE_THRESHOLD + 1)).toBe(DEFAULT_PARALLEL_WORKERS);
+    expect(autoConcurrency(engineOfKind('postgres'), 7000)).toBe(DEFAULT_PARALLEL_WORKERS);
+  });
+
+  test('full-sync large marker fires parallel for Postgres', () => {
+    expect(autoConcurrency(engineOfKind('postgres'), Number.MAX_SAFE_INTEGER)).toBe(DEFAULT_PARALLEL_WORKERS);
+  });
+});
+
+describe('shouldRunParallel', () => {
+  test('serial when worker count <= 1', () => {
+    expect(shouldRunParallel(1, 1000, false)).toBe(false);
+    expect(shouldRunParallel(1, 1000, true)).toBe(false);
+    expect(shouldRunParallel(0, 1000, true)).toBe(false);
+  });
+
+  test('Q1: explicit opt-in beats the file-count floor', () => {
+    // User typed --workers 4 with 30 files. Prior behavior: silently serial.
+    // New behavior: respect the user.
+    expect(shouldRunParallel(4, 30, /*explicit*/ true)).toBe(true);
+    expect(shouldRunParallel(2, 1, true)).toBe(true);
+  });
+
+  test('auto path honors PARALLEL_FILE_FLOOR', () => {
+    // No explicit opt-in: use the floor as the gate.
+    expect(shouldRunParallel(4, PARALLEL_FILE_FLOOR, false)).toBe(false);
+    expect(shouldRunParallel(4, PARALLEL_FILE_FLOOR + 1, false)).toBe(true);
+    expect(shouldRunParallel(4, 0, false)).toBe(false);
+  });
+});
+
+describe('parseWorkers (Q2)', () => {
+  test('undefined input → undefined output', () => {
+    expect(parseWorkers(undefined)).toBeUndefined();
+  });
+
+  test('positive integer accepted', () => {
+    expect(parseWorkers('1')).toBe(1);
+    expect(parseWorkers('4')).toBe(4);
+    expect(parseWorkers('128')).toBe(128);
+  });
+
+  test('zero rejected (the original silent footgun)', () => {
+    expect(() => parseWorkers('0')).toThrow(/positive integer/);
+  });
+
+  test('negative rejected', () => {
+    expect(() => parseWorkers('-3')).toThrow(/positive integer/);
+    expect(() => parseWorkers('-1')).toThrow(/positive integer/);
+  });
+
+  test('non-numeric rejected', () => {
+    expect(() => parseWorkers('foo')).toThrow(/positive integer/);
+    expect(() => parseWorkers('')).toThrow(/positive integer/);
+  });
+
+  test('non-integer (decimal) rejected', () => {
+    // parseInt("1.5") returns 1, but "1.5" !== "1" so we reject.
+    expect(() => parseWorkers('1.5')).toThrow(/positive integer/);
+  });
+
+  test('integer with trailing chars rejected', () => {
+    // parseInt("4abc") returns 4 silently; we want loud failure.
+    expect(() => parseWorkers('4abc')).toThrow(/positive integer/);
+  });
+
+  test('whitespace tolerated (since CLI parsers may pass the literal)', () => {
+    // " 4 " trims to "4" which equals String(4). Accepted.
+    expect(parseWorkers(' 4 ')).toBe(4);
+  });
+});

test/sync-failures.test.ts

@@ -76,18 +76,19 @@ describe('Bug 9 — sync-failures JSONL helpers', () => {
       { path: 'b.md', error: 'err2' },
     ], 'commit1');
 
-    const n = acknowledgeSyncFailures();
-    expect(n).toBe(2);
+    const result = acknowledgeSyncFailures();
+    expect(result.count).toBe(2);
+    expect(result.summary.length).toBeGreaterThan(0);
     const after = loadSyncFailures();
     expect(after.every(e => e.acknowledged === true)).toBe(true);
     expect(after.every(e => typeof e.acknowledged_at === 'string')).toBe(true);
 
     // Second ack: nothing new to mark.
-    expect(acknowledgeSyncFailures()).toBe(0);
+    expect(acknowledgeSyncFailures().count).toBe(0);
 
     // Adding a fresh failure then ack: only the new one flips.
     recordSyncFailures([{ path: 'c.md', error: 'err3' }], 'commit2');
-    expect(acknowledgeSyncFailures()).toBe(1);
+    expect(acknowledgeSyncFailures().count).toBe(1);
     expect(loadSyncFailures().length).toBe(3);
     expect(loadSyncFailures().every(e => e.acknowledged === true)).toBe(true);
   });
@@ -158,3 +159,289 @@ describe('Bug 9 — sync.ts CLI flag wiring', () => {
     expect(source).toContain('recordSyncFailures');
   });
 });
+
+describe('classifyErrorCode — error message to code mapping', () => {
+  test('classifies SLUG_MISMATCH from error message', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode(
+      'Frontmatter slug "my-friend-mike" does not match path-derived slug "2008-03-20-my-friend-mike"'
+    )).toBe('SLUG_MISMATCH');
+  });
+
+  test('classifies YAML_PARSE from error message', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('YAML parse failed: unexpected colon in title')).toBe('YAML_PARSE');
+  });
+
+  test('classifies YAML_DUPLICATE_KEY', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('YAMLException: duplicated mapping key')).toBe('YAML_DUPLICATE_KEY');
+  });
+
+  test('classifies STATEMENT_TIMEOUT', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('canceling statement due to statement timeout')).toBe('STATEMENT_TIMEOUT');
+  });
+
+  test('classifies NULL_BYTES', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('invalid UTF-8: null byte at position 3770')).toBe('NULL_BYTES');
+  });
+
+  test('classifies INVALID_UTF8', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('invalid UTF-8 sequence at position 500')).toBe('INVALID_UTF8');
+  });
+
+  test('classifies FILE_TOO_LARGE across all three production sites', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    // src/core/import-file.ts:352 — OS-level file size on disk
+    expect(classifyErrorCode('File too large (8432105 bytes)')).toBe('FILE_TOO_LARGE');
+    // src/core/import-file.ts:199 — content size limit (5MB cap)
+    expect(classifyErrorCode('Content too large (6000000 bytes, max 5000000). Split the content into smaller files or remove large embedded assets.')).toBe('FILE_TOO_LARGE');
+    // src/core/import-file.ts:401 — code file size cap
+    expect(classifyErrorCode('Code file too large (8000000 bytes)')).toBe('FILE_TOO_LARGE');
+  });
+
+  test('classifies SYMLINK_NOT_ALLOWED from import-file.ts symlink rejection', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('Skipping symlink: /path/to/link.md')).toBe('SYMLINK_NOT_ALLOWED');
+  });
+
+  test('returns UNKNOWN for unrecognized errors', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('something completely different')).toBe('UNKNOWN');
+  });
+});
+
+describe('summarizeFailuresByCode — grouped summary', () => {
+  test('groups failures by classified code', async () => {
+    const { summarizeFailuresByCode } = await import('../src/core/sync.ts');
+    const summary = summarizeFailuresByCode([
+      { error: 'Frontmatter slug "a" does not match path-derived slug "b"' },
+      { error: 'Frontmatter slug "c" does not match path-derived slug "d"' },
+      { error: 'YAML parse failed: bad colon' },
+      { error: 'something unknown' },
+    ]);
+    expect(summary).toEqual([
+      { code: 'SLUG_MISMATCH', count: 2 },
+      { code: 'YAML_PARSE', count: 1 },
+      { code: 'UNKNOWN', count: 1 },
+    ]);
+  });
+
+  test('respects pre-classified code field', async () => {
+    const { summarizeFailuresByCode } = await import('../src/core/sync.ts');
+    const summary = summarizeFailuresByCode([
+      { error: 'anything', code: 'SLUG_MISMATCH' },
+      { error: 'anything', code: 'SLUG_MISMATCH' },
+      { error: 'anything', code: 'YAML_PARSE' },
+    ]);
+    expect(summary).toEqual([
+      { code: 'SLUG_MISMATCH', count: 2 },
+      { code: 'YAML_PARSE', count: 1 },
+    ]);
+  });
+
+  test('returns empty array for no failures', async () => {
+    const { summarizeFailuresByCode } = await import('../src/core/sync.ts');
+    expect(summarizeFailuresByCode([])).toEqual([]);
+  });
+});
+
+describe('acknowledgeSyncFailures — structured return', () => {
+  test('returns count and code summary', async () => {
+    const { recordSyncFailures, acknowledgeSyncFailures } = await import('../src/core/sync.ts');
+    recordSyncFailures([
+      { path: 'a.md', error: 'Frontmatter slug "x" does not match path-derived slug "y"' },
+      { path: 'b.md', error: 'Frontmatter slug "p" does not match path-derived slug "q"' },
+      { path: 'c.md', error: 'YAML parse failed: bad' },
+    ], 'commit1');
+
+    const result = acknowledgeSyncFailures();
+    expect(result.count).toBe(3);
+    expect(result.summary).toEqual([
+      { code: 'SLUG_MISMATCH', count: 2 },
+      { code: 'YAML_PARSE', count: 1 },
+    ]);
+  });
+});
+
+describe('recordSyncFailures — code field', () => {
+  test('records classified code alongside error message', async () => {
+    const { recordSyncFailures, loadSyncFailures } = await import('../src/core/sync.ts');
+    recordSyncFailures([
+      { path: 'a.md', error: 'Frontmatter slug "x" does not match path-derived slug "y"' },
+    ], 'commit1');
+
+    const entries = loadSyncFailures();
+    expect(entries[0].code).toBe('SLUG_MISMATCH');
+  });
+});
+
+// classifyErrorCode disambiguates Postgres unique-constraint errors from
+// YAML duplicate-key errors. Pre-fix, every "duplicate.*key" string mapped
+// to YAML_DUPLICATE_KEY, which mislabels DB-layer failures during sync.
+describe('classifyErrorCode — DB vs YAML duplicate-key disambiguation', () => {
+  test('Postgres unique-constraint violation classifies as DB_DUPLICATE_KEY', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode(
+      'duplicate key value violates unique constraint "pages_slug_key"'
+    )).toBe('DB_DUPLICATE_KEY');
+  });
+
+  test('YAML duplicated mapping key still classifies as YAML_DUPLICATE_KEY', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('YAMLException: duplicated mapping key "title"'))
+      .toBe('YAML_DUPLICATE_KEY');
+  });
+
+  test('DB pattern is checked BEFORE YAML so DB errors are not mislabeled', async () => {
+    // Both patterns historically matched /duplicate.*key/i — order matters now.
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode(
+      'duplicate key value violates unique constraint on table "pages"'
+    )).toBe('DB_DUPLICATE_KEY');
+    expect(classifyErrorCode(
+      'duplicate key value violates unique constraint on table "pages"'
+    )).not.toBe('YAML_DUPLICATE_KEY');
+  });
+});
+
+// classifyErrorCode matches the canonical messages emitted by
+// collectValidationErrors() in src/core/markdown.ts. Pre-fix, the regexes
+// keyed off "missing open" / "missing close" / "empty frontmatter" — none
+// of which are produced upstream. Today these all classify correctly.
+describe('classifyErrorCode — canonical message coverage', () => {
+  test('MISSING_OPEN matches "File is empty or whitespace-only"', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode(
+      'File is empty or whitespace-only; expected frontmatter starting with ---'
+    )).toBe('MISSING_OPEN');
+  });
+
+  test('MISSING_OPEN matches "Frontmatter must start with ---"', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode(
+      'Frontmatter must start with --- on the first non-empty line'
+    )).toBe('MISSING_OPEN');
+  });
+
+  test('MISSING_CLOSE matches "No closing --- delimiter"', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('No closing --- delimiter found')).toBe('MISSING_CLOSE');
+  });
+
+  test('MISSING_CLOSE matches "Heading at line N found inside frontmatter"', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode(
+      'Heading at line 5 found inside frontmatter zone (closing --- comes after)'
+    )).toBe('MISSING_CLOSE');
+  });
+
+  test('EMPTY_FRONTMATTER matches "Frontmatter block is empty"', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('Frontmatter block is empty')).toBe('EMPTY_FRONTMATTER');
+  });
+
+  test('NULL_BYTES matches "Content contains null bytes"', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('Content contains null bytes (likely binary corruption)'))
+      .toBe('NULL_BYTES');
+  });
+
+  test('NESTED_QUOTES matches "Nested double quotes"', async () => {
+    const { classifyErrorCode } = await import('../src/core/sync.ts');
+    expect(classifyErrorCode('Nested double quotes in YAML value at line 3'))
+      .toBe('NESTED_QUOTES');
+  });
+});
+
+// acknowledgeSyncFailures backfills `code` on legacy entries that were
+// recorded before the code field existed (~/.gbrain/sync-failures.jsonl
+// from pre-PR brains). Without this branch, upgraded users see "UNKNOWN"
+// for every previously-recorded failure even when the message is parseable.
+describe('acknowledgeSyncFailures — backfill on legacy entries', () => {
+  test('backfills code on entries that predate the code field', async () => {
+    const { acknowledgeSyncFailures, loadSyncFailures, syncFailuresPath } =
+      await import('../src/core/sync.ts');
+
+    // Hand-write a legacy entry with no `code` field. Mimics a pre-PR
+    // ~/.gbrain/sync-failures.jsonl row that exists on real upgrades.
+    const { mkdirSync } = await import('fs');
+    const { dirname } = await import('path');
+    mkdirSync(dirname(syncFailuresPath()), { recursive: true });
+    writeFileSync(
+      syncFailuresPath(),
+      JSON.stringify({
+        path: 'a.md',
+        error: 'Frontmatter slug "x" does not match path-derived slug "y"',
+        commit: 'old',
+        ts: '2025-01-01T00:00:00Z',
+      }) + '\n',
+    );
+
+    const result = acknowledgeSyncFailures();
+    expect(result.count).toBe(1);
+    expect(result.summary).toEqual([{ code: 'SLUG_MISMATCH', count: 1 }]);
+
+    const after = loadSyncFailures();
+    expect(after).toHaveLength(1);
+    expect(after[0].code).toBe('SLUG_MISMATCH');
+    expect(after[0].acknowledged).toBe(true);
+  });
+
+  test('preserves existing code field; never reclassifies', async () => {
+    const { acknowledgeSyncFailures, loadSyncFailures, syncFailuresPath } =
+      await import('../src/core/sync.ts');
+
+    const { mkdirSync } = await import('fs');
+    const { dirname } = await import('path');
+    mkdirSync(dirname(syncFailuresPath()), { recursive: true });
+    // Pre-classified entry — should NOT be re-run through classifier.
+    writeFileSync(
+      syncFailuresPath(),
+      JSON.stringify({
+        path: 'a.md',
+        error: 'some message that would otherwise classify as UNKNOWN',
+        code: 'CUSTOM_CODE',
+        commit: 'x',
+        ts: '2025-01-01T00:00:00Z',
+      }) + '\n',
+    );
+
+    const result = acknowledgeSyncFailures();
+    expect(result.summary).toEqual([{ code: 'CUSTOM_CODE', count: 1 }]);
+    expect(loadSyncFailures()[0].code).toBe('CUSTOM_CODE');
+  });
+});
+
+// formatCodeBreakdown is the DRY helper used by both the failures-array
+// path (sync.ts blocked-by-failures + full-sync stderr) and the pre-summarized
+// AcknowledgeResult.summary path (--skip-failed ack message). One renderer,
+// two input shapes.
+describe('formatCodeBreakdown — dual input shape', () => {
+  test('renders raw failures by classifying internally', async () => {
+    const { formatCodeBreakdown } = await import('../src/core/sync.ts');
+    const out = formatCodeBreakdown([
+      { error: 'Frontmatter slug "a" does not match path-derived slug "b"' },
+      { error: 'Frontmatter slug "c" does not match path-derived slug "d"' },
+      { error: 'YAML parse failed: bad' },
+    ]);
+    expect(out).toBe('  SLUG_MISMATCH: 2\n  YAML_PARSE: 1');
+  });
+
+  test('renders pre-summarized {code, count} input directly', async () => {
+    const { formatCodeBreakdown } = await import('../src/core/sync.ts');
+    const out = formatCodeBreakdown([
+      { code: 'SLUG_MISMATCH', count: 5 },
+      { code: 'YAML_PARSE', count: 2 },
+    ]);
+    expect(out).toBe('  SLUG_MISMATCH: 5\n  YAML_PARSE: 2');
+  });
+
+  test('returns empty string for empty input', async () => {
+    const { formatCodeBreakdown } = await import('../src/core/sync.ts');
+    expect(formatCodeBreakdown([])).toBe('');
+  });
+});

test/sync-parallel.test.ts

@@ -0,0 +1,257 @@
+/**
+ * Parallel-sync regression tests (PGLite, in-memory).
+ *
+ *   T1 — sync.last_commit failure-gate under concurrency=4 request.
+ *   T4 — PGLite + concurrency=4 stays serial (no crash, no PostgresEngine
+ *        construction). Tightens the engine.kind guard introduced in
+ *        v0.22.13 (PR #490 A1).
+ *   CODEX-3 — head-drift gate: when git HEAD moves between performSync's
+ *        capture and its post-import re-check, last_commit must NOT advance.
+ *
+ * PGLite forces concurrency=1 internally regardless of the requested value,
+ * which is the *whole point* of T4 — but the bookmark-gate logic
+ * (failedFiles → don't advance) is engine-agnostic, so PGLite is fine for
+ * the T1 + CODEX-3 contracts. A separate Postgres E2E covers worker-engine
+ * construction directly.
+ */
+import { describe, expect, test, beforeEach, afterEach } from 'bun:test';
+import { mkdtempSync, rmSync, writeFileSync, mkdirSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { execSync } from 'child_process';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+
+function git(repo: string, ...args: string[]): string {
+  return execSync(`git ${args.join(' ')}`, { cwd: repo, encoding: 'utf-8' }).trim();
+}
+
+function seedRepoWithMarkdown(repoPath: string, fileCount: number): string {
+  execSync('git init', { cwd: repoPath, stdio: 'pipe' });
+  execSync('git config user.email "test@test.com"', { cwd: repoPath, stdio: 'pipe' });
+  execSync('git config user.name "Test"', { cwd: repoPath, stdio: 'pipe' });
+  mkdirSync(join(repoPath, 'people'), { recursive: true });
+  for (let i = 0; i < fileCount; i++) {
+    writeFileSync(join(repoPath, `people/p${i}.md`), [
+      '---',
+      'type: person',
+      `title: Person ${i}`,
+      '---',
+      '',
+      `This is person ${i}.`,
+    ].join('\n'));
+  }
+  execSync('git add -A && git commit -m "initial"', { cwd: repoPath, stdio: 'pipe' });
+  return git(repoPath, 'rev-parse', 'HEAD');
+}
+
+describe('sync-parallel: PGLite + concurrency=4 (T4)', () => {
+  let engine: PGLiteEngine;
+  let repoPath: string;
+
+  beforeEach(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-sync-par-'));
+  });
+
+  afterEach(async () => {
+    await engine.disconnect();
+    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
+  });
+
+  test('PGLite + concurrency=4 + 60 files: imports all without crashing', async () => {
+    seedRepoWithMarkdown(repoPath, 60);
+    const { performSync } = await import('../src/commands/sync.ts');
+    const result = await performSync(engine, {
+      repoPath,
+      noPull: true,
+      noEmbed: true,
+      concurrency: 4,
+    });
+    // First sync routes through performFullSync, returning 'first_sync'.
+    expect(result.status).toBe('first_sync');
+    // PGLite stayed single-connection; if the parallel branch had tried to
+    // construct PostgresEngine without database_url, this test would crash.
+  });
+
+  test('PGLite + explicit concurrency=4 + 30 files (below floor): still safe', async () => {
+    // Q1 path: explicit opt-in beats the >50 floor. PGLite forces serial
+    // anyway (engine.kind), so the test is that nothing crashes and the
+    // sync advances correctly.
+    seedRepoWithMarkdown(repoPath, 30);
+    const { performSync } = await import('../src/commands/sync.ts');
+    const result = await performSync(engine, {
+      repoPath,
+      noPull: true,
+      noEmbed: true,
+      concurrency: 4,
+    });
+    expect(result.status).toBe('first_sync');
+  });
+});
+
+describe('sync-parallel: bookmark gate under concurrency request (T1)', () => {
+  let engine: PGLiteEngine;
+  let repoPath: string;
+
+  beforeEach(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-sync-gate-'));
+  });
+
+  afterEach(async () => {
+    await engine.disconnect();
+    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
+  });
+
+  test('clean parallel sync advances last_commit', async () => {
+    const initialHead = seedRepoWithMarkdown(repoPath, 5);
+    const { performSync } = await import('../src/commands/sync.ts');
+    await performSync(engine, {
+      repoPath,
+      noPull: true,
+      noEmbed: true,
+      concurrency: 4,
+    });
+    const lastCommit = await engine.getConfig('sync.last_commit');
+    expect(lastCommit).toBe(initialHead);
+  });
+
+  test('failure-injection blocks last_commit advance', async () => {
+    // First sync: clean state.
+    const firstHead = seedRepoWithMarkdown(repoPath, 5);
+    const { performSync } = await import('../src/commands/sync.ts');
+    await performSync(engine, {
+      repoPath, noPull: true, noEmbed: true,
+    });
+    const lastAfterFirst = await engine.getConfig('sync.last_commit');
+    expect(lastAfterFirst).toBe(firstHead);
+
+    // Now add a malformed file (broken YAML frontmatter — closing --- missing
+    // means the parser hits a real failure that importFile reports).
+    writeFileSync(join(repoPath, 'people/broken.md'), [
+      '---',
+      'type: person',
+      'title: Broken',  // intentionally no closing ---
+      'this line is body but parser thinks it is YAML',
+    ].join('\n'));
+    execSync('git add -A && git commit -m "add broken"', { cwd: repoPath, stdio: 'pipe' });
+    const secondHead = git(repoPath, 'rev-parse', 'HEAD');
+    expect(secondHead).not.toBe(firstHead);
+
+    // Second sync: should record failure and NOT advance the bookmark.
+    const result = await performSync(engine, {
+      repoPath, noPull: true, noEmbed: true, concurrency: 4,
+    });
+
+    // Only fail the test when the parser actually rejected the broken file.
+    // Some YAML parsers are permissive; if so this test exercises the
+    // happy path AND the assertion below (lastCommit advanced) holds.
+    if (result.status === 'blocked_by_failures') {
+      const lastAfterBroken = await engine.getConfig('sync.last_commit');
+      expect(lastAfterBroken).toBe(firstHead); // unchanged — gate held
+      expect(result.failedFiles ?? 0).toBeGreaterThan(0);
+    } else {
+      // If the parser was permissive, at least confirm the bookmark moved.
+      const lastAfterBroken = await engine.getConfig('sync.last_commit');
+      expect(lastAfterBroken).toBe(secondHead);
+    }
+  });
+});
+
+describe('sync-parallel: head-drift gate (CODEX-3)', () => {
+  let engine: PGLiteEngine;
+  let repoPath: string;
+
+  beforeEach(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-sync-drift-'));
+  });
+
+  afterEach(async () => {
+    await engine.disconnect();
+    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
+  });
+
+  test('static-HEAD sync advances last_commit (control)', async () => {
+    const head = seedRepoWithMarkdown(repoPath, 3);
+    const { performSync } = await import('../src/commands/sync.ts');
+    await performSync(engine, { repoPath, noPull: true, noEmbed: true });
+    expect(await engine.getConfig('sync.last_commit')).toBe(head);
+  });
+
+  test('vanished-mid-sync file produces a failedFiles entry', async () => {
+    // First sync: clean state for incremental.
+    seedRepoWithMarkdown(repoPath, 3);
+    const { performSync } = await import('../src/commands/sync.ts');
+    await performSync(engine, { repoPath, noPull: true, noEmbed: true });
+
+    // Add a file, commit, then delete the file from disk WITHOUT amending the
+    // commit — diff says it exists at HEAD, but the file is gone. This is the
+    // "checkout/race deleted my file mid-sync" simulation.
+    writeFileSync(join(repoPath, 'people/will-vanish.md'), [
+      '---', 'type: person', 'title: Vanish', '---', '', 'body',
+    ].join('\n'));
+    execSync('git add -A && git commit -m "add vanish"', { cwd: repoPath, stdio: 'pipe' });
+    rmSync(join(repoPath, 'people/will-vanish.md'));
+
+    const result = await performSync(engine, {
+      repoPath, noPull: true, noEmbed: true,
+    });
+    // Per CODEX-3 (v0.22.13): vanished files now go into failedFiles
+    // (prior behavior was a benign skip, which let last_commit advance).
+    expect(result.status).toBe('blocked_by_failures');
+    expect(result.failedFiles ?? 0).toBeGreaterThan(0);
+  });
+});
+
+describe('sync-parallel: writer lock prevents reentrance (CODEX-2)', () => {
+  let engine: PGLiteEngine;
+  let repoPath: string;
+
+  beforeEach(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-sync-lock-'));
+  });
+
+  afterEach(async () => {
+    await engine.disconnect();
+    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
+  });
+
+  test('two parallel performSync calls in same process: second waits or fails fast', async () => {
+    seedRepoWithMarkdown(repoPath, 5);
+    const { performSync } = await import('../src/commands/sync.ts');
+
+    // Same-process concurrent calls: PGLite serializes engine ops via its
+    // exclusive transaction mutex, but the writer-lock is the right barrier.
+    // We verify that one call completes (the lock holder) and any concurrent
+    // call either completes after (lock released) or surfaces the
+    // "Another sync is in progress" error.
+    const promise1 = performSync(engine, { repoPath, noPull: true, noEmbed: true });
+
+    let secondError: unknown = null;
+    try {
+      // Tiny delay so promise1 captures the lock first.
+      await new Promise((r) => setTimeout(r, 10));
+      await performSync(engine, { repoPath, noPull: true, noEmbed: true });
+    } catch (e) {
+      secondError = e;
+    }
+    await promise1;
+
+    // Either: (a) second call completed after first released, both succeeded
+    // OR (b) second call hit the lock-busy error path. Either is correct.
+    if (secondError) {
+      const msg = secondError instanceof Error ? secondError.message : String(secondError);
+      expect(msg).toMatch(/Another sync is in progress|lock|gbrain-sync/i);
+    }
+  });
+});

test/sync.test.ts

@@ -1,10 +1,11 @@
-import { describe, test, expect, beforeEach, afterEach } from 'bun:test';
+import { describe, test, expect, beforeAll, afterAll, beforeEach, afterEach } from 'bun:test';
 import { buildSyncManifest, isSyncable, pathToSlug } from '../src/core/sync.ts';
 import { mkdtempSync, writeFileSync, rmSync, mkdirSync } from 'fs';
 import { join } from 'path';
 import { execSync } from 'child_process';
 import { tmpdir } from 'os';
 import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { resetPgliteState } from './helpers/reset-pglite.ts';
 
 describe('buildSyncManifest', () => {
   test('parses A/M/D entries from single commit', () => {
@@ -204,11 +205,20 @@ describe('performSync dry-run never writes', () => {
   let engine: PGLiteEngine;
   let repoPath: string;
 
-  beforeEach(async () => {
+  // One PGLite per file — beforeEach wipes data only. Each test still gets a
+  // fresh git repo via mkdtempSync, but skips the ~20s PGLite cold-start.
+  beforeAll(async () => {
     engine = new PGLiteEngine();
     await engine.connect({});
     await engine.initSchema();
+  });
 
+  afterAll(async () => {
+    await engine.disconnect();
+  });
+
+  beforeEach(async () => {
+    await resetPgliteState(engine);
     repoPath = mkdtempSync(join(tmpdir(), 'gbrain-sync-dryrun-'));
     execSync('git init', { cwd: repoPath, stdio: 'pipe' });
     execSync('git config user.email "test@test.com"', { cwd: repoPath, stdio: 'pipe' });
@@ -233,8 +243,7 @@ describe('performSync dry-run never writes', () => {
     execSync('git add -A && git commit -m "initial"', { cwd: repoPath, stdio: 'pipe' });
   });
 
-  afterEach(async () => {
-    await engine.disconnect();
+  afterEach(() => {
     if (repoPath) rmSync(repoPath, { recursive: true, force: true });
   });