fix(thin-client): keep ambient scope out of get_skill's non-scope source_id param

get_skill's source_id is a mode switch (host catalog vs brain-resident-pack
lookup), not a read-scope filter. Ambient GBRAIN_SOURCE / .gbrain-source
injection would silently reroute 'gbrain skill <name>' on thin clients to
getResidentSkillDetail. Exclude it via NON_SCOPE_SOURCE_ID_OPS; explicit
--source-id still passes through, explicit --source errors with a hint.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

.gitattributes

@@ -1,16 +0,0 @@
-# Line-ending policy.
-#
-# Shell scripts MUST be checked out with LF endings on every platform.
-# Git for Windows installs with `core.autocrlf=true` by default, which
-# rewrites LF -> CRLF on checkout. A strict bash (WSL, Linux CI, macOS)
-# then chokes on the trailing CR:
-#
-#   scripts/run-unit-parallel.sh: line 23: $'\r': command not found
-#   scripts/run-unit-parallel.sh: line 24: set: pipefail : invalid option name
-#   scripts/run-unit-parallel.sh: line 32: syntax error near unexpected token `$'{\r''
-#
-# That silently disabled `bun run test`, `bun run verify`, `bun run ci:local`
-# and `bun run test:e2e` for Windows contributors, since all four dispatch
-# through bash. `eol=lf` pins the checkout regardless of the user's
-# core.autocrlf setting.
-*.sh text eol=lf

.github/workflows/actionlint.yml

@@ -28,5 +28,5 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 5
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: rhysd/actionlint@393031adb9afb225ee52ae2ccd7a5af5525e03e8  # v1.7.11

.github/workflows/e2e.yml

@@ -45,7 +45,7 @@ jobs:
           --health-timeout 5s
           --health-retries 5
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13
@@ -82,7 +82,7 @@ jobs:
           --health-timeout 5s
           --health-retries 5
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13
@@ -116,7 +116,7 @@ jobs:
           --health-timeout 5s
           --health-retries 5
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13

.github/workflows/heavy-tests.yml

@@ -55,7 +55,7 @@ jobs:
           --health-timeout 5s
           --health-retries 5
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13

.github/workflows/release.yml

@@ -24,7 +24,7 @@ jobs:
       id-token: write      # for attest-build-provenance (Sigstore OIDC)
       attestations: write  # for attest-build-provenance
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13
@@ -49,7 +49,7 @@ jobs:
         with:
           path: artifacts
       - name: Create release
-        uses: softprops/action-gh-release@3bb12739c298aeb8a4eeaf626c5b8d85266b0e65  # v2
+        uses: softprops/action-gh-release@153bb8e04406b158c6c84fc1615b65b24149a1fe  # v2
         with:
           files: |
             artifacts/gbrain-darwin-arm64/gbrain-darwin-arm64

.github/workflows/semgrep.yml

@@ -26,7 +26,7 @@ jobs:
     container:
       image: semgrep/semgrep:1.170.0@sha256:c98f8829eea377274ee4b10656458b078b88232469b2ff913f091c2317347c9d
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       # Non-blocking initially (continue-on-error): the first runs establish a
       # baseline without failing unrelated PRs. Graduation path: once the
       # baseline findings are triaged (fixed or `# nosemgrep`'d), remove

.github/workflows/test.yml

@@ -43,7 +43,7 @@ jobs:
       hit: ${{ steps.lookup.outputs.cache-hit }}
       hash: ${{ steps.compute.outputs.hash }}
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - name: Compute content hash
         id: compute
         run: |
@@ -84,7 +84,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
         with:
           fetch-depth: 0
       - uses: gitleaks/gitleaks-action@dcedce43c6f43de0b836d1fe38946645c9c638dc  # v2
@@ -103,7 +103,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 12
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13
@@ -124,7 +124,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13
@@ -149,7 +149,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 12
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13
@@ -172,7 +172,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 12
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13
@@ -206,17 +206,13 @@ jobs:
     needs: cache-check
     if: needs.cache-check.outputs.hit != 'true'
     runs-on: ubuntu-latest
-    # 22, not 15: under parallel PR load the PGLite WASM cold-starts stretch a
-    # shard past 15 min while every test is still passing — the timeout then
-    # cancels the job and the test-status gate reads it as a failure. 13 runs
-    # died this way on 2026-07-21/22 alone.
-    timeout-minutes: 22
+    timeout-minutes: 15
     strategy:
       fail-fast: false
       matrix:
         shard: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
     steps:
-      - uses: actions/checkout@11d5960a326750d5838078e36cf38b85af677262  # v4
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5  # v4
       - uses: oven-sh/setup-bun@0c5077e51419868618aeaa5fe8019c62421857d6  # v2
         with:
           bun-version: 1.3.13

.gitignore

@@ -1,7 +1,4 @@
-# No trailing slash: a bare `node_modules/` pattern matches directories only,
-# so a *symlink* named node_modules slips past it and can be committed
-# (that's how the /tmp-pointing symlink in faf5cdba got in). Match any type.
-node_modules
+node_modules/
 bin/
 .DS_Store
 *.log
@@ -18,7 +15,7 @@ supabase/.temp/
 # self-contained binaries (the bun --compile path embeds it via
 # `import path from 'admin/dist/index.html' with { type: 'file' }`).
 # Build via: cd admin && bun install && bun run build.
-admin/node_modules
+admin/node_modules/
 .idea
 eval/reports/
 eval/data/world-v1/world.html
@@ -38,11 +35,6 @@ export/
 # .context/test-shards/. Workspace-local by design — never committed.
 .context/
 
-# Local agent instruction overrides (CLAUDE.local.md / AGENTS.local.md) — personal,
-# per-clone, loaded after the committed CLAUDE.md/AGENTS.md. Never committed.
-CLAUDE.local.md
-AGENTS.local.md
-
 # Tier 3 PGLite snapshot fixture (built on demand by build:pglite-snapshot)
 test/fixtures/pglite-snapshot.tar
 test/fixtures/pglite-snapshot.version

CHANGELOG.md

@@ -2,296 +2,6 @@
 
 All notable changes to GBrain will be documented in this file.
 
-## [0.42.67.0] - 2026-07-28
-
-**If you develop GBrain on Windows, the test and check commands now actually run. Until this release they were quietly doing almost nothing.**
-
-`bun run test`, `bun run verify`, `bun run ci:local` and `bun run test:e2e` all hand off to shell scripts, and on Windows that hand-off was broken in two separate places. The commands did not stop with an obvious error. They reported a result, so a run could look finished when barely any of the checks had actually inspected anything. On a clean Windows clone, `bun run verify` got 1 check to pass and 31 to fail. It now gets 25 to pass and 7 to fail, and none of the 7 are caused by this change.
-
-The first problem was line endings. Git for Windows installs with `core.autocrlf=true`, which rewrites shell scripts to Windows line endings when you clone or check out. Bash refuses to run those, so a script died on its second line before doing any work. The scripts stored in the repository were always correct; only the copy on your disk was wrong. A new `.gitattributes` pins every `.sh` file to Unix line endings at checkout, no matter how your Git is configured.
-
-The second problem was how the checks were started. Thirty three of them pointed straight at a `.sh` file. On macOS and Linux the shell reads the `#!/usr/bin/env bash` line at the top of the script and runs it correctly. Bun on Windows does not do that, so those commands failed the moment they were called. They now go through `bash` explicitly, the same way the other eleven were already written.
-
-Nothing changes for macOS and Linux. No stored file content moves, and no check behaves differently on those platforms.
-
-## To take advantage of v0.42.67.0
-
-Only Windows contributors need to do anything, and only once. `.gitattributes` applies at checkout time, so shell scripts already sitting on your disk keep their old line endings until you refresh them.
-
-1. **Refresh the working copy** from the repository root:
-   ```bash
-   git rm --cached -r . -q
-   git reset --hard
-   ```
-2. **Confirm bash can read the scripts:**
-   ```bash
-   bash -n scripts/run-unit-parallel.sh
-   ```
-   Silence means it worked. `$'\r': command not found` means step 1 did not take effect.
-3. **Run the gate:**
-   ```bash
-   bun run verify
-   ```
-
-### Itemized changes
-
-- New root `.gitattributes` pins `*.sh text eol=lf`, so shell scripts check out with Unix line endings regardless of the contributor's `core.autocrlf` setting. All 59 tracked `.sh` files were already stored with Unix endings, so `git add --renormalize .` reports nothing to do and no stored content changes.
-- `package.json` now routes the remaining 33 `.sh` check commands through `bash`, matching the 11 that already did. Every tracked `.sh` file carries a bash shebang (52 `#!/usr/bin/env bash` and 7 `#!/bin/bash`), so the treatment is uniform across all of them.
-- The five `scripts/*.ts` entries still run under bun and are untouched.
-- `CONTRIBUTING.md` gains a Windows section covering the one-time working-copy refresh and the `bash scripts/<name>.sh` convention for new checks.
-- `docs/TESTING.md` records how the test commands dispatch through bash, and notes that three tree-walking checks plus `typecheck` can exceed the 120s per-check cap on Windows while passing on Linux and macOS.
-
-## [0.42.66.1] - 2026-07-27
-
-### Fixed
-
-- `gbrain doctor` now treats embedding columns wider than pgvector's HNSW limit as healthy exact-scan configurations instead of prescribing an index PostgreSQL cannot build.
-- Local CI now passes an empty Docker mount list correctly and compiles the embedded-WASM smoke binary from container-local storage on Docker Desktop.
-
-## [0.42.66.0] - 2026-07-24
-
-**54 verified fixes from the community backlog: background enrichment stops wasting money on dead pages, autopilot stops killing its own healthy runs, and search respects your settings.**
-
-This release is the second big sweep through the open pull-request backlog, with every change reviewed and tested individually before merging. The theme is trust in the background machinery. The overnight "dream" cycle now remembers which pages produced nothing and stops re-reading them every night, meters its small-model calls against your spend caps, and keeps claim proposals from silently overwriting each other. Long consolidation runs get a 30-minute deadline instead of being killed at 10 minutes mid-work. A wedged server boot now releases its database lock instead of blocking every later command.
-
-Search behaves the way you configured it: the recency-decay setting now actually applies to hybrid search, a local `list_pages` call returns as many rows as you asked for, and when a listing is cut short it says so instead of looking complete. Slack conversation exports parse cleanly, with an optional AI fallback for formats the parser does not know.
-
-New provider recipes: DashScope reranking, OpenRouter reranking, and a claude-cli recipe for dispatching subagents through the gateway.
-
-## To take advantage of v0.42.66.0
-
-`gbrain upgrade` should do this automatically. One schema migration ships in this release (v125, take-proposal idempotency); it is idempotent and needs no manual action.
-
-1. **Upgrade and verify:**
-   ```bash
-   gbrain upgrade
-   gbrain doctor
-   gbrain stats
-   ```
-2. **If `gbrain doctor` warns about a partial migration**, run the orchestrator manually:
-   ```bash
-   gbrain apply-migrations --yes
-   ```
-3. **If any step fails,** please file an issue at https://github.com/garrytan/gbrain/issues with the output of `gbrain doctor` and `~/.gbrain/upgrade-errors.jsonl` if it exists.
-
-### Itemized changes
-
-#### Dream cycle, takes, and spend control
-
-- Pages whose extraction yields zero claims are memoized, so the cycle stops re-spending on them every night. (#2514, #3319, contributed by @ivandebot)
-- Zero-yield pages are tombstoned so `extract_atoms` stops rediscovering them. (#2144, #3304, contributed by @ChenyqThu)
-- `extract_atoms` Haiku calls are metered against the cost gate. (#2371, #3329, contributed by @TheRealMrSystem)
-- `extract_atoms` stamps concepts so `synthesize_concepts` has material to work with. (#2123, #3308, contributed by @ChenyqThu)
-- `extract_facts` requires a live backing page, not just a non-NULL entity slug. (#2497, #3321, contributed by @javieraldape)
-- Multi-claim pages keep every proposal instead of only the first (migration v125 makes the idempotency key per claim). (#3297, contributed by @rp-agent-bot)
-- Superseding a take now queries the active row first. (#3275, contributed by @arisgysel-design)
-- Takes keyword search matches words inside long claims via `word_similarity`. (#3267)
-- Dream-generated orphan pages stay scoped to their source. (#2368, #3344, contributed by @snvtac)
-- Drift detection is wired into the dream cycle, report-only for now. (#2653, #3317)
-
-#### Autopilot, jobs, and serve
-
-- Full consolidation cycles get a 30-minute timeout floor; lighter dispatches keep the interval-derived budget. (#2852, #3338, contributed by @sanchalr)
-- The cron wrapper exports `~/.bun/bin` onto PATH so autopilot survives minimal environments. (#2013, #3305, contributed by @klampatech)
-- Dead or cancelled jobs no longer block idempotent re-submission. (#2253, #3306, contributed by @rafaelreis-r)
-- Contextual reindex jobs get a default timeout. (#2611, #3323, contributed by @spiky02plateau)
-- Onboarding stops repeating the same auto-remediation within a single run. (#2854, #3342, contributed by @sanchalr)
-- A wedged `gbrain serve` boot hits a readiness deadline and releases the PGLite lock. (#3335)
-
-#### Search, retrieval, and health
-
-- The recency-decay config is honored on the hybrid search path. (#2386, #3312, contributed by @rwbaker)
-- `list_pages` honors explicit limits for local callers, warns on remote clamping, and threads `offset`. (#2591, #3322, contributed by @deacon-botdoctor)
-- Truncated `list_pages` results say so instead of silently capping. (#2865, #3341, contributed by @paul-0320)
-- Negative metrics no longer invert trajectory regression signals. (#2621, #3324, contributed by @morluto)
-- Per-chunk synopsis generation in contextual retrieval is concurrency-bounded. (#2628, #3326, contributed by @spiky02plateau)
-- Graph health metrics count `entity` pages. (#2639, #3330, contributed by @tylr-r)
-
-#### Ingestion, extraction, and links
-
-- Conversation parsing gains an opt-in LLM fallback for unknown formats. (#2247, #3371, contributed by @danwiggins)
-- Normalized Slack markdown parses into conversations. (#3289, #3372, contributed by @danwiggins)
-- Conversation backfill outcomes are durable, so completed pages skip on the next run. (#3293, #3373, contributed by @danwiggins)
-- Reference-style wikilinks are recognized during extraction. (#2071, #3303, contributed by @mzkarami)
-- `[[wikilink]]` frontmatter values resolve via global basename lookup. (#2406, #3313, contributed by @spiky02plateau)
-- Incremental push syncs extract links. (#2850, #3337, contributed by @patentsong)
-- `<think>` reasoning tags in extractor output are handled. (#2559, #3318, contributed by @qaz8545355)
-- Tiktoken special tokens no longer crash code-chunker token estimates. (#2453, #3315, contributed by @Jiglet)
-- Source config stops re-wrapping into a growing JSON string scalar. (#2829, #3334, contributed by @1alessio)
-
-#### Providers and recipes
-
-- DashScope reranking recipe (DashScope serves a plural `/reranks` endpoint under its compatible API). (#2644, #3328, contributed by @YiconZiwei)
-- OpenRouter reranking touchpoint. (#2164, #3302, contributed by @Hippityy)
-- claude-cli recipe for native gateway-based subagent dispatch. (#2277, #3310, contributed by @brettdavies)
-- Prefixed model IDs work on the openai-compatible embedding-dimensions path. (#2325, #3309, contributed by @noetherly)
-- Embeddings stamp the gateway-resolved model in `content_chunks.model`, not the compiled default. (#2846, #3343, contributed by @SailorJoe6)
-- Bun-on-Windows write-through EEXIST fixed, non-Anthropic `--max-cost` pricing works, dream pages excluded from enrich. (#2407, #3316, contributed by @nguyenchiviet)
-- Supabase signed URLs prepend `/storage/v1`. (#2565, #3320, contributed by @danwiggins)
-
-#### Sources, auth, and multi-brain
-
-- Federated-source pages are visible to `get_page`, `list_pages`, `resolve_slugs`, and no-grant MCP callers. (#3242, #3301)
-- Admin-gated rescope surface for DCR clients stuck on a default scope. (#3299)
-- `whoami` exposes OAuth source grants. (#3279, #3332, contributed by @boundless-forest)
-- Thin-client `--source` maps onto `source_id` for remote-routed operations. (#3086)
-
-#### CLI, doctor, and init
-
-- `gbrain doctor` stops claiming "Brain is at target" when the target is unreachable. (#2151, #3339, contributed by @brettdavies)
-- Doctor gains a raw-source persistence guarantee for synthesized pages, warn-only for now. (#3300)
-- Doctor timeline labels disambiguate entity coverage from the brain-score component. (#2298, #3073, contributed by @TurgutKural)
-- Unknown `gbrain init` flags are rejected before migrations run. (#2201, #3307, contributed by @caioribeiroclw-pixel)
-- The init soul-audit hint points at the conversational skill, not a nonexistent CLI verb. (#2486, #3314, contributed by @SeanGearin)
-- `--force` retry escapes completed migration-ledger entries. (#2616, #3325, contributed by @spiky02plateau)
-- PGLite data-dir lock contention gets a clear error message. (#2658, #3336, contributed by @zaycruz)
-- Frontmatter validation derives slugs from the brain root, not the absolute path. (#2340, #3311, contributed by @alessioalionco)
-
-#### For contributors
-
-- Docker network isolation guidance for co-located self-hosted Postgres. (#3270, #3331)
-- `CLAUDE.local.md` / `AGENTS.local.md` are gitignored. (#3290, contributed by @igbymyboy)
-- The hybrid-reranker integration test isolates `GBRAIN_HOME`. (#1527, #3327, contributed by @Willisbest)
-- Test-shard scripts capture the real exit code before watchdog teardown in the no-timeout fallback. (#2864, #3340, contributed by @paul-0320)
-
-## [0.42.65.0] - 2026-07-23
-
-**A large maintenance release: 93 verified fixes and small features merged since v0.42.64.0, most of them community contributions.**
-
-If you use gbrain day to day, this release makes the boring parts trustworthy. Importing and syncing notes is safer: a failed pull no longer pretends everything is up to date, imported pages are read back after writing to confirm they landed, and a page with real content can no longer be silently overwritten by an empty one. Search answers get better inputs: the think command now picks excerpts that actually match your question, and results respect your federated source settings. Background enrichment (the "dream" cycle) wastes less money and retries properly when an AI provider is down. Spending caps now fail closed, so a billing hiccup can never turn into an uncapped spend. And `gbrain doctor` is quieter, with several false alarms removed and real problems (like an embedding backlog with no worker running) now flagged.
-
-More AI providers work out of the box, including OpenRouter prompt caching, MiniMax and Zhipu GLM recipes, Ollama Matryoshka embedding dimensions, and llama-server batch limits.
-
-## To take advantage of v0.42.65.0
-
-`gbrain upgrade` should do this automatically. No new schema migrations ship in this release.
-
-1. **Upgrade and verify:**
-   ```bash
-   gbrain upgrade
-   gbrain doctor
-   gbrain stats
-   ```
-2. **If `gbrain doctor` reports new findings after upgrading,** that is the quieter, more accurate check set working as intended. Each finding names its fix.
-3. **If any step fails,** please file an issue at https://github.com/garrytan/gbrain/issues with the output of `gbrain doctor` and `~/.gbrain/upgrade-errors.jsonl` if it exists.
-
-### Itemized changes
-
-#### Security
-
-- MCP source scoping for remote callers got a hardening pass, so agent-facing connections stay confined to the sources they were granted. (#2881, contributed by @spinsirr)
-- Paid MCP spend accounting is now atomic and fails closed, and resolver spend is recorded before a cap error is raised, so caps cannot be raced past or undercounted. (#3203, #3204, contributed by @caterpillarC15)
-- The OAuth token endpoint rate limit on the HTTP server is now configurable via env for deployments behind shared IPs. (#3114, contributed by @time-attack)
-- `WWW-Authenticate` responses now carry `resource_metadata` per the MCP spec and RFC 9728, so conforming clients can discover the auth server. (#1410, contributed by @rayers)
-
-#### Search, retrieval, and think
-
-- `think` selects query-relevant excerpts instead of generic ones. (#3197, contributed by @Y0lan)
-- Unqualified local CLI `search`/`query` now honors `sources.config.federated` read visibility. (#2561, #3141, contributed by @time-attack)
-- Email citation metadata is projected into search results. (#2873, contributed by @amtagrwl)
-- The `think` Gaps section renders once instead of twice. (#1662, contributed by @howwohmm)
-- Fuzzy entity lookup threads the caller's source scope and skips soft-deleted entities. (#1508, contributed by @tim404x)
-- `code-def` surfaces method, constructor, field, and struct definitions, not just top-level symbols. (#1628, contributed by @rayers)
-- Briefing pages are excluded from their own Brain Pulse salience. (#1202, contributed by @rwbaker)
-- Reranker calls with missing auth are classified as configuration errors before falling back. (#2059, #3139, contributed by @time-attack)
-
-#### Import, sync, and ingestion
-
-- A failed git pull with zero imports reports `partial (pull_failed)` instead of `up_to_date`. (#3068, #3253, contributed by @Masashi-Ono0611)
-- Imports run a post-write read-back verification with a durable ingest-log record. (#2869, contributed by @Andredsouza1984)
-- `put` refuses to overwrite a non-empty page with empty content. (#2708, contributed by @symmetric-matthew)
-- `putPage` restores soft-deleted rows instead of colliding with them. (#2779, contributed by @RerankerGuo)
-- Mixed-case slugs are normalized before chunk upsert, ending duplicate-chunk churn. (#430, #3143, contributed by @time-attack)
-- Imports fall back to the body H1 for the title when frontmatter lacks `title:`. (#2446, #3072, contributed by @time-attack)
-- YAML comments inside the frontmatter fence are no longer treated as markdown headings. (#3225, #3247, contributed by @Masashi-Ono0611)
-- Write-through guards case-insensitive filesystem collisions before the atomic write. (#2831, #3119, contributed by @time-attack)
-- Path-qualified wikilinks outside the known directory pattern resolve on the DB/put_page path. (#2866, contributed by @paul-0320)
-- CJK slugs are supported in the slug registry and dream-cycle summary slugs. (#782, #738, #3083, contributed by @time-attack)
-- Three ingest/sync/serve singleton fixes: page-type round-trip, deleted-slug embed noise, and a stateless width guard. (#3140, contributed by @time-attack)
-- Sync honors the `embedding_disabled` sentinel as an implicit `--no-embed`. (#2879, contributed by @gawievanblerk)
-- Verified sync head sentinels are cleared correctly. (#2734, contributed by @symmetric-matthew)
-- Resumed syncs report the pinned commit they actually landed on. (#3202, contributed by @caterpillarC15)
-- The expected `discover_git_root` probe failure stays off stderr. (#3232, contributed by @Masashi-Ono0611)
-- `extract --stale` runs the real resolver so basename resolution reaches stale pages, and clears pre-version-bump pages. (#2576, #2717, contributed by @paul-0320; #1791, contributed by @Nazim22)
-- Oversized code chunks are capped so they stay embeddable, and code-chunk metadata survives re-embeds. (#1675, contributed by @lubosxyz; #769, #1232, contributed by @rayers)
-
-#### Background cycle, dream, and facts
-
-- Path-derived dream sources are stamped, and the engine closes cleanly on autopilot shutdown. (#3178, contributed by @time-attack)
-- All-provider-failed atom drains propagate so durable jobs retry instead of silently dropping work. (#3218, #3248, contributed by @Masashi-Ono0611)
-- Atom extraction raises `maxTokens` and case-normalizes `atom_type` for Gemini models. (#3211, contributed by @alexey-metaengage)
-- The conversation extractor gates anonymous-speaker self-attribution instead of guessing. (#3228, contributed by @asenkovskiy)
-- Incremental dream extraction stamps its watermark so re-runs stop reprocessing. (#2636, #3115, contributed by @time-attack)
-- `dream --dry-run --json` keeps stdout clean of embed summaries. (#394, #3109, contributed by @time-attack)
-- Synthesized dream pages require a self-contained opening summary. (#2770, contributed by @Masashi-Ono0611)
-- PGLite inline synth subagent drains complete, and `lint` gains `--exclude`. (#2699, #2649, #3162, contributed by @time-attack)
-- Live context reads the documented "P1 Today" heading form with plain checkbox tasks, matching the daily-task-manager skill's output format. (#2186, #3124, contributed by @time-attack)
-- Queued AI jobs refresh gateway config at execution time instead of using a stale snapshot. (#2125, contributed by @maxpetrusenkoagent)
-- `brainstorm`/`propose_takes` honor configured models: cost preview uses the configured model, the judge reads its config key, provider probes are skipped when unneeded, and page projection is narrowed. (#3120, contributed by @time-attack)
-- Backlog hardening wave: x-to-brain health check, propose_takes deadlines, capture title truncation, extract_atoms backlog handling, and pooler direct-URL routing. (#3165, contributed by @time-attack)
-- `skillopt` emits `proposed.md` in no-mutate mode. (#2635, #3182, contributed by @time-attack)
-- Nightly quality probe enable path and conversation-parser probe are wired up. (#2629, #2630, #3094, contributed by @time-attack)
-
-#### Doctor, health, and maintenance
-
-- New safe maintenance automation with a shared orphan-exclusion policy, so routine cleanup runs without risking linked content. (#3015, #3023, contributed by @time-attack)
-- `orphan_ratio` excludes the chronicle volume under `life/events/`. (#2264, #3214, contributed by @asenkovskiy)
-- `brain_score` orphan/timeline components use the orphans-audit linkable scope. (#3155, contributed by @time-attack)
-- Entity timeline coverage is measured separately from whole-brain density. (#2761, contributed by @TurgutKural)
-- Doctor flags embed backfills queued with no worker running. (#2696, contributed by @javieraldape)
-- Two doctor false-positive/timeout fixes: the drift walk skips `node_modules`, and the bare-tweet check skips inline code and cited lines. (#1772, contributed by @sonlndv)
-- A dead `llm_fallback_enabled` recommendation is dropped from conversation format coverage. (#1903, contributed by @ElliotDrel)
-- Skill triggers with CRLF line endings parse on Windows. (#1149, contributed by @samporter-31)
-- Onboard check names are registered in doctor categories, ending unknown-check warnings, and onboard-check remediations survive the `--apply --auto` path. (#3075, #3097, contributed by @time-attack)
-- Dead slug prefixes are counted by slug. (#2697, contributed by @RerankerGuo)
-- The backlinks worker defaults to check, not fix, and `check-backlinks` honors its positional directory argument. (#1853, contributed by @choomz; #3076, contributed by @time-attack)
-- Calibration resolves the owner holder via config, defaulting to `self`. (#3077, contributed by @time-attack)
-- Memory throttling on Linux reads `/proc/meminfo` MemAvailable. (#556, contributed by @chengzehsu)
-
-#### AI providers and gateway
-
-- OpenRouter gets family-scoped prompt caching, and query expansion works on chat-capable openai-compat recipes. (#3152, contributed by @time-attack)
-- MiniMax recipe: embedding wire-shape compat fetch plus a chat touchpoint. (#1977, #3089, contributed by @time-attack)
-- The Zhipu recipe gains a chat touchpoint so GLM subagents work. (#1157, #3084, contributed by @time-attack)
-- Tier-configured models reach the recipe allowlist, Anthropic model lists are refreshed, tier resolutions are registered, and probe labels are honest. (#2800, contributed by @p3ob7o)
-- Provider base URL config merges from the DB. (#1676, contributed by @TheLordArgus)
-- The gateway falls back to the pooler when the derived direct host is unreachable. (#1641, #3088, contributed by @time-attack)
-- Config-plane `voyage_api_key` folds into `VOYAGE_API_KEY` like the other hosted keys. (#3236, contributed by @Masashi-Ono0611)
-- The `zeroentropyai:zerank-2` reranker has a pricing entry so the budget tracker can meter it. (#3223, #3233, contributed by @Masashi-Ono0611)
-- llama-server embedding batches are capped at its 32-input request limit. (#1281, contributed by @mmekkaoui)
-- Matryoshka dimensions thread through for Qwen3-Embedding on Ollama. (#1072, contributed by @mgandal)
-- `init` seeds AI options from env on cold install, and `whoami` reports the stdio transport. (#3091, contributed by @time-attack)
-- The `models` dispatch subcommand reads its first argument correctly. (#1428, contributed by @BenjaminDSmithy)
-- Synopsis generation tail-truncates document text for small-model chat handlers. (#1427, contributed by @BenjaminDSmithy)
-- The contradiction judge token cap is raised for thinking models. (#3210, contributed by @alexey-metaengage)
-
-#### Schema, migrations, and storage engines
-
-- Engine migration counts and surfaces per-page copy failures instead of silently advancing. (#3241, contributed by @Masashi-Ono0611)
-- Invalid `CONCURRENTLY`-build index remnants are dropped without a DO block. (#3191, contributed by @Masashi-Ono0611)
-- Unsupported large-dimension HNSW indexes are skipped instead of failing schema setup. (#1734, #3080, contributed by @time-attack)
-- The v0.32.2 migration dirty-check scopes to targeted sources and surfaces failed phase detail. (#3093, contributed by @time-attack)
-- Schema packs merge the full `extends` chain and `borrow_from` into the resolved manifest. (#1749, #3181, contributed by @time-attack)
-- The schema-pack stats catch-all is narrowed so masked errors surface instead of fake zero-page counts. (#2466, #3133, contributed by @time-attack)
-- Bundled schema-pack inspection reports the pack actually shipped in the binary, and minion subagent auth resolves through config. (#3110, contributed by @time-attack)
-- PGLite `putPage` guards against zero-row RETURNING. (#1649, contributed by @alexhawkins)
-
-#### MCP server and CLI surface
-
-- `list_pages` rows include `source_id`. (#3209, contributed by @alexey-metaengage)
-- Running CLI commands while `gbrain serve` (MCP) holds the brain now notifies about the conflict instead of failing confusingly. (#3243, contributed by @fdefitte)
-- The OpenClaw plugin manifest entry is declared so the plugin loads. (#2551, #3185, contributed by @time-attack)
-
-#### For contributors
-
-- CI scanner roots are normalized on macOS. (#3198, contributed by @caterpillarC15)
-- CI shard timeout raised to 22 minutes plus a delta-assert reporter leak test. (#3231, contributed by @time-attack)
-- E2E suite hardening: flaky tests, no-op assertions, and cross-test coupling removed. (#1704, contributed by @auroracapital)
-- `mechanical.test.ts` isolates `$HOME` so the E2E suite stops clobbering user config. (#434, contributed by @lloydarmbrust)
-- The lint code-fence-wrap detector and fixer regex now agree. (#1597, contributed by @chungty)
-- README project links for OpenClaw and Hermes are corrected. (#1961, #3179, contributed by @time-attack)
-- A completed TODOS entry is dropped. (#3229, contributed by @Masashi-Ono0611)
-
 ## [0.42.64.0] - 2026-07-20
 
 ### Fixed

CONTRIBUTING.md

@@ -11,28 +11,6 @@ bun test
 
 Requires Bun 1.0+.
 
-### Windows
-
-`bun run test`, `verify`, `ci:local` and `test:e2e` all dispatch through bash, so
-the shell scripts under `scripts/` must be checked out with Unix line endings.
-The root `.gitattributes` pins `*.sh text eol=lf`, which overrides the
-`core.autocrlf=true` that Git for Windows installs by default. A fresh clone is
-correct with no extra steps.
-
-If you cloned before that pin existed, your working copy still has the old
-Windows line endings and bash will fail with `$'\r': command not found`. Refresh
-it once, from the repository root:
-
-```bash
-git rm --cached -r . -q
-git reset --hard
-bash -n scripts/run-unit-parallel.sh   # silence means bash can read the scripts
-```
-
-Every `check:*` entry in `package.json` invokes its script as `bash scripts/<name>.sh`
-rather than relying on the shebang, because bun on Windows cannot exec a `.sh`
-directly. Keep that prefix when you add a new shell-script check.
-
 ## Project structure
 
 ```
@@ -185,14 +163,6 @@ host port with `GBRAIN_CI_PG_PORT=5435 bun run ci:local` if 5434 collides.
 Fail-closed selector: an unmapped `src/` change runs all 29 E2E files. Hand-tune
 narrower mappings via `scripts/e2e-test-map.ts`.
 
-### PR-side security checks
-
-Besides the test gate, PRs may trigger three security workflows: Semgrep CE
-SAST (every PR — **advisory/non-blocking** while the baseline is tuned, so a
-Semgrep finding won't fail your PR), OSV-Scanner (only when `package.json` or
-`bun.lock` change), and actionlint (only when `.github/workflows/**` change).
-See `SECURITY.md` → "Automated security scanning" for details.
-
 ## Building
 
 ```bash

README.md

@@ -71,8 +71,8 @@ GBrain is designed to be installed and operated by an AI agent. The fastest path
 
 If you don't already have an AI agent platform running, start with one of these. Both are designed to read GBrain's install protocol and execute it:
 
-- **[OpenClaw](https://github.com/openclaw/openclaw)** — deploy [AlphaClaw on Render](https://render.com/deploy?repo=https://github.com/chrysb/alphaclaw) (one click, 8GB+ RAM)
-- **[Hermes](https://github.com/NousResearch/hermes-agent)** — deploy on [Railway](https://github.com/praveen-ks-2001/hermes-agent-template) (one click)
+- **[OpenClaw](https://github.com/openclawagents/openclaw)** — deploy [AlphaClaw on Render](https://render.com/deploy?repo=https://github.com/chrysb/alphaclaw) (one click, 8GB+ RAM)
+- **[Hermes](https://github.com/openclawagents/hermes)** — deploy on [Railway](https://github.com/praveen-ks-2001/hermes-agent-template) (one click)
 
 Then paste this into your agent:
 

SECURITY.md

@@ -8,30 +8,6 @@ on GitHub.
 
 Do not open a public issue for security vulnerabilities.
 
-## Automated security scanning
-
-CI runs three automated security checks alongside secret scanning (Gitleaks):
-
-- **Dependency vulnerabilities** — OSV-Scanner
-  (`.github/workflows/osv-scanner.yml`) runs weekly and on any PR that touches
-  `package.json` or `bun.lock`.
-- **Static analysis (SAST)** — Semgrep CE (`.github/workflows/semgrep.yml`)
-  runs on every PR and weekly. It is currently **advisory (non-blocking)**
-  while the finding baseline is tuned; the graduation path to a blocking check
-  is documented in the workflow file.
-- **Release binary provenance** — release builds
-  (`.github/workflows/release.yml`) attest each compiled binary with
-  [GitHub artifact attestations](https://docs.github.com/en/actions/security-for-github-actions/using-artifact-attestations).
-  Verify a downloaded release binary with:
-
-  ```bash
-  gh attestation verify ./gbrain-darwin-arm64 -R garrytan/gbrain
-  gh attestation verify ./gbrain-linux-x64 -R garrytan/gbrain
-  ```
-
-All security workflows use SHA-pinned actions and least-privilege permissions,
-enforced structurally by actionlint on every workflow change.
-
 ## Remote MCP Security
 
 ### ⚠️ Do NOT use open OAuth client registration for remote MCP
@@ -159,18 +135,6 @@ 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.
 
-### Docker network isolation (self-hosted Postgres)
-
-OAuth and source scoping enforce isolation on the `serve --http` path only.
-Raw Postgres reachability bypasses both: a container that shares Docker's
-default `bridge` network with the brain's Postgres can open a direct DB
-session without any token and read every source. Put the brain's Postgres on
-a user-defined Docker network with nothing untrusted on it, publish its port
-loopback-only (if at all), and never put `DATABASE_URL` or a Postgres
-password in untrusted agent containers — those should reach the brain
-exclusively via OAuth against `serve --http`. Full operator checklist:
-[docs/mcp/DEPLOY.md — Co-located Docker workloads](docs/mcp/DEPLOY.md#co-located-docker-workloads-self-hosted-postgres).
-
 ### CORS
 
 Default-deny: no `Access-Control-Allow-Origin` header is sent unless an

TODOS.md

@@ -1,31 +1,18 @@
 # TODOS
 
-## v0.42.67.0 follow-ups (Windows build tooling)
-
-Filed as follow-ups from v0.42.67.0 (`.gitattributes` LF pin for `*.sh` +
-`bash` prefix on the 33 `package.json` check commands). Both items are newly
-observable: before that release these checks never executed on Windows at all,
-so nothing about their runtime was measurable.
-
-- [ ] **P2 — three guard scripts exceed the 120s `run-verify-parallel.sh` cap on Windows.**
-  With the dispatch fixed, `bun run verify` on Windows gets 25 passes and 7 failures, and
-  `check:privacy`, `check:test-names` and `check:test-isolation` are timeouts rather than
-  real failures (they pass on Linux and macOS well inside the cap). They walk the tree with
-  per-file shell loops, which is far slower under Windows process creation. Either raise the
-  cap for these three, or replace the per-file loop with a single `grep -r` pass. Same cap
-  swallows `typecheck`, though standalone `bun run typecheck` exits 0.
-- [ ] **P3 — `check:wasm` cannot create its `node_modules` symlink on Windows.**
-  `scripts/check-wasm-embedded.sh` fails with `ln: failed to create symbolic link
-  '/tmp/gbrain-wasm-check.XXXX/node_modules': No such file or directory`. Unprivileged
-  Windows accounts cannot create symlinks without developer mode. Consider a junction, a
-  copy, or skipping the check with a clear message when symlink creation is unavailable.
-
 ## community fix-wave follow-ups (filed v0.42.60.0)
 
-- [x] **P2 — cherry-pick #2112's uncovered doctor.ts hunk.** Fix-wave A (#2820) superseded
+- [ ] **P1 — take-writes source scoping fails open when source resolution errors (#2684 residual).**
+  `resolveTakesSourceId` (src/commands/takes.ts) swallows resolution errors and returns
+  `undefined`, which falls back to the unscoped slug-only page lookup — so an invalid
+  `GBRAIN_SOURCE` (or a broken dotfile chain) silently restores the pre-#2698 cross-source
+  write behavior on multi-source brains. Decide fail-closed semantics: error out when a
+  source was explicitly requested but doesn't resolve; keep the unscoped fallback only for
+  brains with no source configuration at all. Add a regression test for the invalid-source
+  path. Found by cross-model adversarial review during the v0.42.60.0 release ship.
+- [ ] **P2 — cherry-pick #2112's uncovered doctor.ts hunk.** Fix-wave A (#2820) superseded
   most of #2112 but not its `checkSubagentCapability` fix (check explicit `models.subagent`
-  before `models.tier.subagent`). Implemented: `checkSubagentCapability` now resolves
-  `models.subagent` before tier/default fallbacks and has regression coverage.
+  before `models.tier.subagent`). Refile or cherry-pick; the rest of that PR is covered.
 
 ## v0.42.59.0 follow-ups (five-fix rollup #2735–#2739)
 
@@ -82,20 +69,17 @@ Deferred from the provider-agnostic plumbing wave (#1249/#1250/#1292/#2271/#2209
 Plan + review trail at `~/.claude/plans/system-instruction-you-are-working-keen-newell.md`.
 The eng-review + Codex outside-voice narrowed the wave to these deferrals:
 
-- [x] **P2 — Capability-aware query expansion on OpenAI-compat providers (#2372).**
+- [ ] **P2 — Capability-aware query expansion on OpenAI-compat providers (#2372).**
   Expansion only runs for recipes that declare an `expansion` touchpoint, and only the
   native providers (anthropic/openai/google) do. To make expansion work on
   litellm/openrouter/groq/together/deepseek you must ADD expansion touchpoints to those
   chat-capable recipes AND add a `generateObject`→`generateText` capability fallback for
   backends without strict structured outputs. Feature-shaped; overlaps the general
   OpenAI-compat proxy story (`docs/designs/COMMUNITY_IDEAS.md`). Community PR #2373 is a
-  starting point. Implemented by #2373 plus the DeepSeek/Groq/Together recipe wave,
-  LiteLLM chat/expansion support, and the OpenRouter expansion touchpoint. Where:
-  `src/core/ai/gateway.ts:expand`, recipe files, `types.ts` (ExpansionTouchpoint).
-- [x] **P2 — LiteLLM as a chat/expansion backend.** `litellm-proxy` declares ONLY an
+  starting point. Where: `src/core/ai/gateway.ts:expand`, recipe files, `types.ts` (ExpansionTouchpoint).
+- [ ] **P2 — LiteLLM as a chat/expansion backend.** `litellm-proxy` declares ONLY an
   embedding touchpoint, so `think`/chat on LiteLLM is dead. Add chat (and expansion) so a
-  LiteLLM proxy is a full LLM backend, not embedding-only. Implemented by #2208.
-  The general OpenAI-compat proxy story.
+  LiteLLM proxy is a full LLM backend, not embedding-only. The general OpenAI-compat proxy story.
 - [ ] **P3 — Per-model embedding dims metadata on `EmbeddingTouchpoint`.** `default_dims`
   is recipe-wide, so a recipe (ollama) can't carry different native dims per model. This
   wave added the modern ollama model NAMES + a `trust_custom_dims` passthrough (user supplies
@@ -2303,25 +2287,10 @@ at plan time and got carved out:
   via `buildPerSourceBindings`. Document workaround: register
   source-scoped OAuth clients.
 
-- [x] **v0.41+: T20 — extends-chain merging in registry.ts.** DONE (#1749).
-  `resolvePack` now merges parent → child (child-wins) for the six
-  ingest/query-shaping fields (`page_types`, `link_types`,
-  `frontmatter_links`, `enrichable_types`, `filing_rules`, `takes_kinds`)
-  plus `borrow_from` materialization, in `src/core/schema-pack/merge.ts`.
-  The cascade was transparent (consumers already read `resolved.manifest`),
-  not per-consumer. `phases`/`calibration_domains` deliberately excluded —
-  see the P3 follow-up below.
-
-- [ ] **P3: explicit opt-in to inherit `phases` / `calibration_domains`.**
-  T20 excludes these two from the child-wins merge because they gate real
-  cycle execution (`cycle.ts` `packDeclaresPhase`) and the manifest
-  contract says each pack declares its own participation explicitly —
-  auto-inheriting would silently make a child run cycle phases it never
-  requested. Multi-level lens packs (`gbrain-everything`) therefore still
-  re-declare them by hand. If that redeclaration becomes painful, add an
-  explicit manifest flag (e.g. `inherit_phases: true`) so a pack author
-  opts in consciously. Depends on: T20 (landed). Start in
-  `src/core/schema-pack/merge.ts` (`mergeInheritedManifest`).
+- [ ] **v0.41+: T20 — extends-chain merging in registry.ts.**
+  `registry.ts:167` documents the gap. Implementing full child-wins
+  merge cascades through every consumer of `manifest.page_types`. ~1
+  day CC.
 
 - [ ] **v0.41+: T21 — comment-preserving YAML emitter.**
   v0.40.7.0 emitter does NOT preserve comments. Authors who care

VERSION

@@ -1 +1 @@
-0.42.67.0
+0.42.64.0

admin/dist/index.html

@@ -7,7 +7,7 @@
   <link rel="preconnect" href="https://fonts.googleapis.com" />
   <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin />
   <link href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600&family=JetBrains+Mono:wght@400;500&display=swap" rel="stylesheet" />
-  <script type="module" crossorigin src="/admin/assets/index-CviJXT-1.js"></script>
+  <script type="module" crossorigin src="/admin/assets/index-CoGEje3-.js"></script>
   <link rel="stylesheet" crossorigin href="/admin/assets/index-GxkWX7v3.css">
 </head>
 <body>

admin/src/api.ts

@@ -39,21 +39,11 @@ export const api = {
   stats: () => apiFetch('/admin/api/stats'),
   health: () => apiFetch('/admin/api/health-indicators'),
   agents: () => apiFetch('/admin/api/agents'),
-  sources: () => apiFetch('/admin/api/sources'),
   requests: (page = 1, qs = '') => apiFetch(`/admin/api/requests?page=${page}${qs}`),
   apiKeys: () => apiFetch('/admin/api/api-keys'),
-  createApiKey(keyName: string) {
-    return apiFetch('/admin/api/api-keys', { method: 'POST', body: JSON.stringify({ name: keyName }) });
-  },
-  revokeApiKey(keyName: string) {
-    return apiFetch('/admin/api/api-keys/revoke', { method: 'POST', body: JSON.stringify({ name: keyName }) });
-  },
+  createApiKey: (name: string) => apiFetch('/admin/api/api-keys', { method: 'POST', body: JSON.stringify({ name }) }),
+  revokeApiKey: (name: string) => apiFetch('/admin/api/api-keys/revoke', { method: 'POST', body: JSON.stringify({ name }) }),
   updateClientTtl: (clientId: string, tokenTtl: number | null) => apiFetch('/admin/api/update-client-ttl', { method: 'POST', body: JSON.stringify({ clientId, tokenTtl }) }),
-  rescopeClient: (clientId: string, sourceId: string, federatedRead: string[]) =>
-    apiFetch('/admin/api/rescope-client', {
-      method: 'POST',
-      body: JSON.stringify({ clientId, sourceId, federatedRead }),
-    }),
   revokeClient: (clientId: string) => apiFetch('/admin/api/revoke-client', { method: 'POST', body: JSON.stringify({ clientId }) }),
   // v0.36.1.0 (T15 / E6) — calibration endpoints.
   calibrationProfile: (holder?: string) =>

admin/src/pages/Agents.tsx

@@ -18,8 +18,6 @@ interface Agent {
   client_name?: string; // compat
   grant_types: string[];
   scope: string;
-  source_id: string | null;
-  federated_read: string[];
   created_at: string;
   last_used_at: string | null;
   total_requests: number;
@@ -28,12 +26,6 @@ interface Agent {
   status: 'active' | 'revoked';
 }
 
-interface Source {
-  id: string;
-  name: string;
-  federated: boolean;
-}
-
 interface ApiKey {
   id: string;
   name: string;
@@ -44,7 +36,6 @@ interface ApiKey {
 
 export function AgentsPage() {
   const [agents, setAgents] = useState<Agent[]>([]);
-  const [sources, setSources] = useState<Source[]>([]);
   const [hideRevoked, setHideRevoked] = useState(true);
   const [showRegister, setShowRegister] = useState(false);
   const [showCredentials, setShowCredentials] = useState<{ clientId: string; clientSecret: string; name: string } | null>(null);
@@ -52,10 +43,7 @@ export function AgentsPage() {
   const [showApiKeyToken, setShowApiKeyToken] = useState<{ name: string; token: string } | null>(null);
   const [selectedAgent, setSelectedAgent] = useState<Agent | null>(null);
 
-  useEffect(() => {
-    loadAgents();
-    api.sources().then(setSources).catch(() => {});
-  }, []);
+  useEffect(() => { loadAgents(); }, []);
 
   const loadAgents = () => { api.agents().then(setAgents).catch(() => {}); };
 
@@ -100,7 +88,6 @@ export function AgentsPage() {
                 <th>Name</th>
                 <th>Type</th>
                 <th>Scopes</th>
-                <th>Sources</th>
                 <th>Status</th>
                 <th>Requests</th>
                 <th>Last Used</th>
@@ -121,11 +108,6 @@ export function AgentsPage() {
                       <span key={s} className={`badge badge-${s}`} style={{ marginRight: 4 }}>{s}</span>
                     ))}
                   </td>
-                  <td style={{ color: 'var(--text-secondary)', fontSize: 12 }}>
-                    {a.auth_type === 'oauth'
-                      ? `${a.source_id || 'none'} · ${(a.federated_read || []).length} readable`
-                      : 'Unscoped'}
-                  </td>
                   <td>
                     <span className={`badge ${a.status === 'active' ? 'badge-success' : 'badge-danger'}`}>{a.status}</span>
                   </td>
@@ -162,21 +144,7 @@ export function AgentsPage() {
       )}
 
       {selectedAgent && (
-        <AgentDrawer
-          key={selectedAgent.id}
-          agent={selectedAgent}
-          sources={sources}
-          onClose={() => setSelectedAgent(null)}
-          onRevoked={loadAgents}
-          onRescoped={({ sourceId, federatedRead }) => {
-            setSelectedAgent(current => current ? {
-              ...current,
-              source_id: sourceId,
-              federated_read: federatedRead,
-            } : current);
-            loadAgents();
-          }}
-        />
+        <AgentDrawer agent={selectedAgent} onClose={() => setSelectedAgent(null)} onRevoked={loadAgents} />
       )}
 
       {showApiKeyCreate && (
@@ -413,127 +381,7 @@ function CredentialsModal({ credentials, onClose }: {
   );
 }
 
-function SourceAccessEditor({ clientId, agent, sources, onRescoped }: {
-  clientId: string;
-  agent: Agent;
-  sources: Source[];
-  onRescoped: (scope: { sourceId: string; federatedRead: string[] }) => void;
-}) {
-  const [writeSource, setWriteSource] = useState(agent.source_id || 'default');
-  const [readSources, setReadSources] = useState<string[]>(agent.federated_read || []);
-  const [saving, setSaving] = useState(false);
-  const [error, setError] = useState('');
-  const [saved, setSaved] = useState(false);
-  const readableSet = new Set(readSources);
-  const activeSourceIds = new Set(sources.map(source => source.id));
-  const unavailableReadSources = readSources.filter(sourceId => !activeSourceIds.has(sourceId));
-  const primaryUnavailable = !activeSourceIds.has(writeSource);
-
-  const save = async () => {
-    if (readSources.length === 0) {
-      setError('Select at least one readable source.');
-      return;
-    }
-    setSaving(true);
-    setError('');
-    setSaved(false);
-    try {
-      const result = await api.rescopeClient(clientId, writeSource, readSources) as {
-        sourceId: string;
-        federatedRead: string[];
-      };
-      setWriteSource(result.sourceId);
-      setReadSources(result.federatedRead);
-      setSaved(true);
-      onRescoped(result);
-    } catch (e) {
-      setError(e instanceof Error ? e.message : 'Failed to save source access');
-    } finally {
-      setSaving(false);
-    }
-  };
-
-  return (
-    <>
-      <div className="section-title">Source Access</div>
-      <div style={{ color: 'var(--text-secondary)', fontSize: 12, lineHeight: 1.5, marginBottom: 12 }}>
-        The primary source is the write destination. Read access is an explicit allowlist and does not widen automatically.
-      </div>
-      <div style={{ marginBottom: 14 }}>
-        <label htmlFor="agent-write-source">Primary / write source</label>
-        <select
-          id="agent-write-source"
-          value={writeSource}
-          onChange={e => { setWriteSource(e.target.value); setSaved(false); }}
-          style={{ width: '100%', background: 'var(--bg-secondary)', color: 'var(--text-primary)', border: '1px solid var(--border)', borderRadius: 6, padding: '6px 10px', fontSize: 14 }}
-        >
-          {primaryUnavailable && (
-            <option value={writeSource} disabled>{writeSource} · unavailable</option>
-          )}
-          {sources.map(source => (
-            <option key={source.id} value={source.id}>{source.name} ({source.id})</option>
-          ))}
-        </select>
-      </div>
-      <fieldset style={{ border: 0, padding: 0, margin: '0 0 14px' }}>
-        <legend>Readable sources</legend>
-        <div className="checkbox-group" style={{ marginTop: 6 }}>
-          {sources.map(source => (
-            <label key={source.id} className="checkbox-label">
-              <input
-                type="checkbox"
-                checked={readableSet.has(source.id)}
-                onChange={e => {
-                  setSaved(false);
-                  setReadSources(current => e.target.checked
-                    ? [...current, source.id]
-                    : current.filter(id => id !== source.id));
-                }}
-              />
-              {source.name} ({source.id}){source.federated ? ' · federated' : ' · private'}
-            </label>
-          ))}
-          {unavailableReadSources.map(sourceId => (
-            <label key={sourceId} className="checkbox-label" style={{ color: 'var(--warning)' }}>
-              <input
-                type="checkbox"
-                checked
-                onChange={() => {
-                  setSaved(false);
-                  setReadSources(current => current.filter(id => id !== sourceId));
-                }}
-              />
-              {sourceId} · unavailable (clear to remove grant)
-            </label>
-          ))}
-        </div>
-      </fieldset>
-      {(primaryUnavailable || unavailableReadSources.length > 0) && (
-        <div style={{ color: 'var(--warning)', fontSize: 13, marginBottom: 10 }}>
-          This client references unavailable or archived sources. Choose an active primary source and clear unavailable read grants before saving.
-        </div>
-      )}
-      {error && <div style={{ color: 'var(--error)', fontSize: 13, marginBottom: 10 }}>{error}</div>}
-      {saved && <div style={{ color: 'var(--success)', fontSize: 13, marginBottom: 10 }}>Source access saved.</div>}
-      <button
-        type="button"
-        className="btn btn-primary"
-        disabled={saving || readSources.length === 0 || sources.length === 0 || primaryUnavailable || unavailableReadSources.length > 0}
-        onClick={save}
-      >
-        {saving ? 'Saving...' : 'Save Source Access'}
-      </button>
-    </>
-  );
-}
-
-function AgentDrawer({ agent, sources, onClose, onRevoked, onRescoped }: {
-  agent: Agent;
-  sources: Source[];
-  onClose: () => void;
-  onRevoked: () => void;
-  onRescoped: (scope: { sourceId: string; federatedRead: string[] }) => void;
-}) {
+function AgentDrawer({ agent, onClose, onRevoked }: { agent: Agent; onClose: () => void; onRevoked: () => void }) {
   const [tab, setTab] = useState<'claude-code' | 'chatgpt' | 'claude-cowork' | 'perplexity' | 'cursor' | 'json'>('claude-code');
   const copy = (text: string) => navigator.clipboard.writeText(text);
   const serverUrl = window.location.origin;
@@ -705,15 +553,6 @@ function AgentDrawer({ agent, sources, onClose, onRevoked, onRescoped }: {
           <span>{agent.token_ttl ? (agent.token_ttl >= 31536000 ? 'No expiry' : agent.token_ttl >= 86400 ? `${Math.floor(agent.token_ttl / 86400)}d` : agent.token_ttl >= 3600 ? `${Math.floor(agent.token_ttl / 3600)}h` : `${agent.token_ttl}s`) : '1h (default)'}</span>
         </div>
 
-        {isOAuth && (
-          <SourceAccessEditor
-            clientId={cid}
-            agent={agent}
-            sources={sources}
-            onRescoped={onRescoped}
-          />
-        )}
-
         {/*
           Config Export visible for both auth_type=oauth AND auth_type=api_key.
           Claude Code + Cursor + JSON tabs render real snippets regardless
@@ -740,11 +579,7 @@ function AgentDrawer({ agent, sources, onClose, onRevoked, onRescoped }: {
         {(() => {
           const oauthOnlyTabs = new Set(['chatgpt', 'claude-cowork', 'perplexity']);
           if (!isOAuth && oauthOnlyTabs.has(tab)) {
-            const clientName = tab === 'chatgpt'
-              ? 'ChatGPT'
-              : tab === 'claude-cowork'
-                ? 'Claude.ai'
-                : 'Perplexity';
+            const clientName = { chatgpt: 'ChatGPT', 'claude-cowork': 'Claude.ai', perplexity: 'Perplexity' }[tab] || tab;
             return (
               <div style={{
                 background: 'rgba(255, 200, 100, 0.08)',

bun.lock

@@ -51,9 +51,8 @@
     "@electric-sql/pglite",
   ],
   "overrides": {
-    "@hono/node-server": "^2.0.5",
-    "body-parser": "^2.3.0",
-    "fast-uri": "^3.1.4",
+    "@hono/node-server": "^1.19.13",
+    "fast-uri": "^3.1.2",
     "fast-xml-builder": "^1.1.7",
     "fast-xml-parser": "^5.7.0",
     "form-data": "^4.0.6",
@@ -163,7 +162,7 @@
 
     "@electric-sql/pglite": ["@electric-sql/pglite@0.4.3", "", {}, "sha512-ichuWTgtd4mOM1G4SpyGJa5trT03lWbMypDV0fUXUCXg5hiHqVAz/bZyV68NqmkLB7WcYmj1RMJVSp8HV/v/ZQ=="],
 
-    "@hono/node-server": ["@hono/node-server@2.0.11", "", { "peerDependencies": { "hono": "^4" } }, "sha512-bjD221KPLoJTWUwso1J6fGKiTXEUFedG/s0visavY4zakFPkeGURMRNly+FhBHs7T8Dz4qHaZIMX9ZoJHSJtKA=="],
+    "@hono/node-server": ["@hono/node-server@1.19.14", "", { "peerDependencies": { "hono": "^4" } }, "sha512-GwtvgtXxnWsucXvbQXkRgqksiH2Qed37H9xHZocE5sA3N8O8O8/8FA3uclQXxXVzc9XBZuEOMK7+r02FmSpHtw=="],
 
     "@jsquash/avif": ["@jsquash/avif@2.1.1", "", { "dependencies": { "wasm-feature-detect": "^1.2.11" } }, "sha512-LMRxd0fMgfCLtobDh0/sFYJMMiRJTNYSEEWvRDKXlAeZ08t3gI5V+1thIT0XjXJ+SVG7Zug9B0XPyx0Ti5VRNA=="],
 
@@ -327,7 +326,7 @@
 
     "asynckit": ["asynckit@0.4.0", "", {}, "sha512-Oei9OH4tRh0YqU3GxhX79dM/mwVgvbZJaSNaRk+bshkj0S5cfHcgYakreBjrHwatXKbz+IoIdYLxrKim2MjW0Q=="],
 
-    "body-parser": ["body-parser@2.3.0", "", { "dependencies": { "bytes": "^3.1.2", "content-type": "^2.0.0", "debug": "^4.4.3", "http-errors": "^2.0.1", "iconv-lite": "^0.7.2", "on-finished": "^2.4.1", "qs": "^6.15.2", "raw-body": "^3.0.2", "type-is": "^2.1.0" } }, "sha512-2cGmJupaNgg+QUwVLAucDuWuoMZ6EX9iHDRswZ5lsNYEmwPaRknMPCLZz07yTzVq/83p4o/wzbDZbBrTvGGTIw=="],
+    "body-parser": ["body-parser@2.2.2", "", { "dependencies": { "bytes": "^3.1.2", "content-type": "^1.0.5", "debug": "^4.4.3", "http-errors": "^2.0.0", "iconv-lite": "^0.7.0", "on-finished": "^2.4.1", "qs": "^6.14.1", "raw-body": "^3.0.1", "type-is": "^2.0.1" } }, "sha512-oP5VkATKlNwcgvxi0vM0p/D3n2C3EReYVX+DNYs5TjZFn/oQt2j+4sVJtSMr18pdRr8wjTcBl6LoV+FUwzPmNA=="],
 
     "bowser": ["bowser@2.14.1", "", {}, "sha512-tzPjzCxygAKWFOJP011oxFHs57HzIhOEracIgAePE4pqB3LikALKnSzUyU4MGs9/iCEUuHlAJTjTc5M+u7YEGg=="],
 
@@ -401,7 +400,7 @@
 
     "fast-deep-equal": ["fast-deep-equal@3.1.3", "", {}, "sha512-f3qQ9oQy9j2AhBe/H9VC91wLmKBCCU/gDOnKNAYG5hswO7BLKj09Hc5HYNz9cGI++xlpDCIgDaitVs03ATR84Q=="],
 
-    "fast-uri": ["fast-uri@3.1.4", "", {}, "sha512-8JnbkQ4juDyvYs4mgFGQqg4yCYtFDtUtmp2QIQq11ZZe5CFQ5wcqm1rqDgAh/QdMySuBnPzMUiJUNZG5N/AiQw=="],
+    "fast-uri": ["fast-uri@3.1.3", "", {}, "sha512-i70LwGWUduXqzicKXWshooq+sWL1K3WUU5rKZNG/0i3a1OSoX3HqhH5WbWwTmqWfor4urUakGPiRQcleRZTwOg=="],
 
     "fast-xml-builder": ["fast-xml-builder@1.3.0", "", { "dependencies": { "path-expression-matcher": "^1.6.2", "xml-naming": "^0.3.0" } }, "sha512-F74cZEdCvuw9P41GAC3rod4X04jjWGM1JPEv/GWSqFTWLsdyMSBMBMlm9Hk3GLBgLBbdBNY8yee0pQh2RBVESQ=="],
 
@@ -615,10 +614,6 @@
 
     "@types/bun/bun-types": ["bun-types@1.3.11", "", { "dependencies": { "@types/node": "*" } }, "sha512-1KGPpoxQWl9f6wcZh57LvrPIInQMn2TQ7jsgxqpRzg+l0QPOFvJVH7HmvHo/AiPgwXy+/Thf6Ov3EdVn1vOabg=="],
 
-    "body-parser/content-type": ["content-type@2.0.0", "", {}, "sha512-j/O/d7GcZCyNl7/hwZAb606rzqkyvaDctLmckbxLzHvFBzTJHuGEdodATcP3yIRoDrLHkIATJuvzbFlp/ki2cQ=="],
-
-    "body-parser/type-is": ["type-is@2.1.0", "", { "dependencies": { "content-type": "^2.0.0", "media-typer": "^1.1.0", "mime-types": "^3.0.0" } }, "sha512-faYHw0anBbc/kWF3zFTEnxSFOAGUX9GFbOBthvDdLsIlEoWOFOtS0zgCiQYwIskL9iGXZL3kAXD8OoZ4GmMATA=="],
-
     "es-set-tostringtag/hasown": ["hasown@2.0.2", "", { "dependencies": { "function-bind": "^1.1.2" } }, "sha512-0hJU9SCPvmMzIBdZFqNPXWa6dqh7WdH0cII9y+CyS8rG3nL48Bclra9HmKhVVUHyPWNH5Y7xDwAB7bfgSjkUMQ=="],
 
     "eventsource/eventsource-parser": ["eventsource-parser@3.0.6", "", {}, "sha512-Vo1ab+QXPzZ4tCa8SwIHJFaSzy4R6SHf7BY79rFBDf0idraZWAkYrDjDj8uWaSm3S2TK+hJ7/t1CEmZ7jXw+pg=="],

docs/INSTALL.md

@@ -39,11 +39,10 @@ gbrain migrate --to pglite       # Postgres → PGLite (rare)
 
 For shared / large / multi-machine deployments (a team or company brain with multiple users hitting one server over HTTP MCP with OAuth scoping per user), follow the dedicated walkthrough: **[Tutorial: set up GBrain as your company brain](tutorials/company-brain.md)**.
 
-API keys live in `~/.gbrain/config.json` (file plane) or env vars (`OPENAI_API_KEY`, `OPENROUTER_API_KEY`, `ZEROENTROPY_API_KEY`, `VOYAGE_API_KEY`, `ANTHROPIC_API_KEY`). Set via CLI:
+API keys live in `~/.gbrain/config.json` (file plane) or env vars (`OPENAI_API_KEY`, `ZEROENTROPY_API_KEY`, `VOYAGE_API_KEY`, `ANTHROPIC_API_KEY`). Set via CLI:
 
 ```bash
 gbrain config set zeroentropy_api_key sk-...
-gbrain config set openrouter_api_key sk-or-...
 gbrain config set anthropic_api_key sk-ant-...
 ```
 

docs/TESTING.md

@@ -19,29 +19,6 @@ Seven test command tiers, each with a clear scope:
 | `bun run test:e2e` | Real Postgres E2E. Requires Docker + `DATABASE_URL`. Sequential. | ~5-10min | Pre-ship; nightly. |
 | `bun run check:all` | The historical pre-check scripts (22, chained sequentially in package.json). Overlaps `verify` heavily but is NOT a superset — `verify`'s `CHECKS` array in `scripts/run-verify-parallel.sh` (~30 entries incl. typecheck) is the authoritative gate; `check:all` keeps a few local-only extras (trailing-newline, exports-count, no-legacy-getconnection). | ~10s | Local-only sweep for the extras. |
 
-### Shell dispatch and Windows
-
-All four of `test`, `verify`, `ci:local` and `test:e2e` hand off to shell scripts
-under `scripts/`, so every `check:*` entry in `package.json` invokes its script as
-`bash scripts/<name>.sh` instead of relying on the shebang — bun on Windows cannot
-exec a `.sh` directly. Add a new shell-script check with that same prefix. The
-`scripts/*.ts` entries run under bun and take no prefix.
-
-The scripts must also be on disk with Unix line endings. A strict bash (WSL, Linux
-CI, macOS) rejects CRLF and dies on the script's first meaningful line; the Cygwin
-bash that ships with Git for Windows tolerates it, so a green local run is not by
-itself evidence that a script is CRLF-clean.
-The root `.gitattributes` pins `*.sh text eol=lf`, which overrides the
-`core.autocrlf=true` default that Git for Windows installs. Working copies cloned
-before that pin need a one-time `git rm --cached -r . -q && git reset --hard` to
-pick it up; see the Windows section of `CONTRIBUTING.md`.
-
-Wallclock figures in the table above are from a Mac dev box. Windows is
-substantially slower because each check pays full process-creation cost, and three
-tree-walking checks (`check:privacy`, `check:test-names`, `check:test-isolation`)
-plus `typecheck` can exceed the 120s per-check cap in `run-verify-parallel.sh`
-there even though they pass on Linux and macOS.
-
 ### CI vs local: intentionally divergent file sets
 
 - **CI matrix** (`.github/workflows/test.yml`) runs `scripts/test-shard.sh` across 10 matrix shards partitioned by weight-aware LPT bin-packing (`scripts/sharding.ts`) and INCLUDES `*.slow.test.ts` (the two outlier slow files run as dedicated jobs alongside the matrix). CI EXCLUDES `*.serial.test.ts` from the shards and runs them in a dedicated job via `bun run test:serial`, one bun process per file — keeping serial files out of the shard processes is what preserves the `mock.module` quarantine (a top-level mock in one file leaks into every other file sharing its process). `bun run verify` gets its own job too. CI is the ground truth for "did everything pass."
@@ -212,10 +189,8 @@ Unit tests and what they cover:
 - `test/orphans.test.ts` — orphans command: detection, pseudo filtering, text/json/count outputs, MCP op.
 - `test/postgres-engine.test.ts` — `statement_timeout` scoping: `sql.begin` + `SET LOCAL` shape, source-level grep guardrail against a reintroduced bare `SET statement_timeout`.
 - `test/sync.test.ts` — sync logic + regression guard asserting top-level `engine.transaction` is not called.
-- `test/sync-pull-failed-anchor.serial.test.ts` — #3068 regression: a failed internal `git pull` (local-path origin vs `protocol.file.allow=never`) with zero imports returns `partial`/`pull_failed` (not `up_to_date`), freezes `last_commit` + `last_sync_at`, recovers after a manual pull; fall-through import of local commits preserved. Serial: pins `GBRAIN_HOME` to a temp dir for the whole file.
 - `test/sync-concurrency.test.ts` — `autoConcurrency()` thresholds + PGLite-forces-serial + explicit-override clamping; `shouldRunParallel()` explicit-bypasses-floor contract; `parseWorkers()` validation rejecting `'0'`/`'-3'`/`'foo'`/`'1.5'`/trailing chars.
 - `test/sync-parallel.test.ts` — PGLite-routed coverage of the bookmark gate under concurrency, head-drift gate, vanished-file failure capture, PGLite-stays-serial, and the `gbrain-sync` writer-lock contract.
-- `test/sync-all-missing-path.test.ts` — `sync --all --missing-path <fail|skip>` pure helpers: `parseMissingPathMode` (default fail, explicit values, loud rejection of bad/dangling values, never swallows a following flag) and `partitionMissingPathSources` (classification driven only by the injected pathExists predicate — no fs; null `local_path` passes through runnable; order preserved).
 - `test/sync-failures.test.ts` — `classifyErrorCode` regex coverage for all 12 codes against literal production message strings from `markdown.ts` and `import-file.ts`; `summarizeFailuresByCode` sort + pre-classified-honor; `recordSyncFailures` code-field persistence; `acknowledgeSyncFailures` `AcknowledgeResult` shape + backfill on legacy entries.
 - `test/doctor.test.ts` — doctor command; assertions that `jsonb_integrity` scans the four JSONB write sites and `markdown_body_completeness` is present.
 - `test/utils.test.ts` — shared SQL utilities + `tryParseEmbedding` null-return and single-warn semantics.

docs/architecture/RETRIEVAL.md

@@ -87,15 +87,6 @@ embedding proximity. Four layers, added after the incident in
   deciding "is this page already here, safe to NOT write a duplicate?" keys off
   `create_safety`, not a raw blended score.
 
-**Extraction quarantine lane (issue #160):** pages carrying the unverified
-auto-extracted markers (frontmatter `provenance: auto-extracted` +
-`status: unverified`, see `src/core/extraction-review.ts`) rank as ordinary
-content — they are skipped by the compiled-truth fusion boost and by the
-`people/`/`companies/` namespace source-boost, and every search result from
-such a page carries `unverified: true` so agents can label the provenance.
-Promote or reject them via `gbrain extraction-pending` / `gbrain
-extraction-review`.
-
 The `search` MCP/CLI op is **cheap-hybrid** (vector + keyword + RRF + pool +
 title + alias, expansion off); `query` is the full-control variant. NamedThingBench
 (`gbrain eval retrieval-quality`) gates these families on every PR. Diagnose a

docs/architecture/conversation-parser-patterns.md

@@ -1,146 +0,0 @@
-# Conversation parser patterns
-
-The conversation parser turns exported chat and meeting transcripts into a
-common message stream without requiring an LLM call for known formats. This
-document describes the built-in pattern contract and the checks required when
-adding or changing a format.
-
-## Data flow
-
-`parseConversation` uses this sequence:
-
-1. Resolve the page date and timezone context.
-2. Score every enabled built-in and user pattern against the first ten
-   non-blank lines.
-3. Re-score the full body when the head score is inconclusive, or when a broad
-   pattern explicitly requires full-body scoring.
-4. Reject the winner when its acceptance score is below the false-positive
-   floor.
-5. Apply the winning pattern to every line and attach continuation lines to the
-   preceding message.
-6. Optionally run LLM polish or fallback when those features are enabled.
-
-Pattern order is only a tie-breaker. A new regex must be structurally distinct
-from neighboring formats; moving it earlier in the registry is not a valid
-non-shadowing strategy.
-
-## Built-in pattern contract
-
-Every `PatternEntry` in `builtins.ts` declares:
-
-- A stable, kebab-case `id`.
-- A hand-vetted line regex and explicit capture-group indexes.
-- Where the date comes from and how the time is represented.
-- A timezone policy.
-- Whether the format supports multi-line message bodies.
-- Positive and negative samples that run during module initialization.
-- A documentation pointer describing the source format.
-
-The registry refuses to load when a positive sample stops matching, a negative
-sample starts matching, or a capture map becomes invalid. This catches local
-regex mistakes before extraction can silently produce empty conversations.
-
-### Date and timezone rules
-
-Formats with an inline date should capture it from each message. Time-only
-formats use an explicit caller fallback first, then the page frontmatter date,
-then the page effective date. If none is available, the parser uses
-`1970-01-01` so the missing date remains visible instead of inventing a current
-date.
-
-Time-only formats normally use `utc_assumed_with_warn`. The parser constructs a
-UTC timestamp and returns a timezone warning when the page does not provide a
-timezone. A new pattern should not imply local-time precision that the source
-format does not contain.
-
-### Multi-line messages
-
-An anchor regex identifies the first line of a message. Subsequent non-anchor
-lines are appended to that message until another anchor appears. Set
-`multi_line: true` when continuation content is part of the documented format,
-such as Markdown bullets, blockquotes, or an exported message body on the next
-line.
-
-Tests for a multi-line format should assert the complete message text, including
-newlines. A message-count assertion alone will not detect lost bullets or a
-continuation attached to the wrong speaker.
-
-### Scoring and false positives
-
-The score compares matched anchors with the pattern's relevant candidate lines.
-The first pass uses the head of the page for speed. Low-confidence pages are
-re-scored across the full body before the parser accepts a winner.
-
-Multi-line formats may opt into `score_continuations_as_body` when their anchor
-grammar is distinctive. Candidate-only scoring activates only after two anchors
-match, or when the first non-blank line is an anchor. This evidence threshold
-lets a single long message keep its continuation body without turning one stray
-anchor in a prose page into a conversation. Candidate anchor lines that fail the
-full regex still lower the score. Other patterns continue to use all non-blank
-lines in their density score.
-
-Use `score_full_body: true` for a broad grammar that also occurs in ordinary
-prose. For example, `**Label:** text` can be either a transcript line or a bold
-label in meeting notes. Narrow formats with a timestamp and a distinctive
-separator generally do not need this override.
-
-`quick_reject` is a performance hint, not an acceptance rule. It should cheaply
-exclude obviously unrelated lines while admitting every string accepted by the
-main regex.
-
-## Normalized Slack Markdown
-
-The `bold-time-dash` pattern parses message anchors shaped like:
-
-```text
-**Alice Example** 09:15 — first message
-- supporting detail
-**Bob Example** 09:18 — second message
-```
-
-Its grammar is:
-
-```text
-**speaker** H:MM <dash> text
-```
-
-where:
-
-- `H:MM` is a valid 24-hour time from `0:00` through `23:59`.
-- `<dash>` may be an em dash (`—`), en dash (`–`), or ASCII hyphen (`-`).
-- The date comes from the resolved page date context.
-- Continuation lines belong to the preceding message.
-- The captured clock value is emitted with `Z`. Timezone metadata suppresses
-  the missing-timezone warning but is not currently used for IANA conversion.
-
-The required time and dash distinguish it from all existing bold-speaker
-formats:
-
-- `**Speaker** (09:15): text` uses `bold-paren-time`.
-- `**Speaker** (9:15 AM): text` uses `bold-paren-time-12h`.
-- `**Speaker:** text` uses `bold-name-no-time`.
-- `**Speaker** (2026-04-09 9:15 AM): text` uses `imessage-slack`.
-
-Keeping these examples in both `test_negative` and parser regression tests makes
-the non-shadowing contract executable.
-
-## Adding a built-in format
-
-1. Collect multiple anonymized examples, including separator and timestamp
-   variants that occur in the same export family.
-2. Choose the narrowest grammar that represents the format. Constrain numeric
-   fields such as hours and minutes when possible.
-3. Add at least two positive module-load samples and negative samples for every
-   neighboring pattern that could plausibly overlap.
-4. Add parser tests that verify speakers, timestamps, text, continuation
-   handling, and non-shadowing behavior.
-5. Add a dedicated JSONL fixture and include the same cases in
-   `test/fixtures/conversation-formats/all.jsonl`.
-6. Run the focused parser tests and the fixture evaluator.
-7. Run the repository verification and full test suites before submission.
-8. Update `docs/architecture/KEY_FILES.md` when the registry count or supported
-   format inventory changes.
-
-Use generic fixture identities such as `Alice Example`, `Bob Example`, and
-`Summary Bot`. Never copy real transcript names or private content into source,
-tests, documentation, commits, or pull-request descriptions.

docs/architecture/lens-packs.md

@@ -75,15 +75,6 @@ Meta-pack stacking creator + investor + engineer via the v0.38
 preserved — this IS the active pack; the registry walks extends +
 borrow to materialize the merged view.
 
-**Merge contract (T20 / #1749).** `resolvePack` merges parent → child
-(child-wins) for the six ingest/query-shaping fields: `page_types`,
-`link_types`, `frontmatter_links`, `enrichable_types`, `filing_rules`,
-and `takes_kinds` (unioned — a child cannot narrow it). `phases` and
-`calibration_domains` are **NOT** inherited: they gate cycle execution,
-so each pack must declare its own participation explicitly. That is why
-`gbrain-everything` re-declares all its phases and all 7
-`calibration_domains` — inheritance does not carry them.
-
 Activate via `gbrain config set schema_pack gbrain-everything` and
 calibration_profile produces all 7 domain scorecards in one JSONB.
 

docs/architecture/pack-upgrade-mechanism.md

@@ -229,7 +229,7 @@ add `GBRAIN_AUDIT_FULL=1` (v0.43+ TODO; not yet wired).
 - Per-source pack-upgrade (the handler accepts `sourceId` but
   `findPackSuccessors` doesn't yet pass it through)
 - Cross-brain federated mounts that disagree on canonical packs
-- Automatic rollback (today: manual SQL or `gbrain restore`)
+- Automatic rollback (today: manual SQL or `gbrain pages restore`)
 - LLM-assisted mapping_rules codegen from production data (`gbrain
   schema detect-mappings`; deferred to v0.43+)
 

docs/architecture/schema-packs.md

@@ -145,7 +145,7 @@ api_version: gbrain-schema-pack-v1
 name: my-pack
 version: 0.0.1
 gbrain_min_version: 0.39.0
-extends: gbrain-base   # inherits base's TYPES (see Merge contract below); add overrides
+extends: gbrain-base   # inherits everything from base; add overrides below
 description: |
   My personal pack.
 
@@ -170,34 +170,6 @@ enrichable_types: []
 filing_rules: []
 ```
 
-## Merge contract (`extends` + `borrow_from`)
-
-`resolvePack` composes a pack against its `extends` chain (and any
-`borrow_from` targets) into the `resolved.manifest` every consumer reads
-(T20 / #1749). The rules:
-
-- **Six fields inherit, child-wins:** `page_types`, `link_types`,
-  `frontmatter_links`, `enrichable_types`, `filing_rules`, and `takes_kinds`.
-  A child value with the same key (type name, link name, etc.) overrides the
-  parent's; keys the child doesn't declare come through from the parent.
-- **`page_types` ordering:** overrides of a base type keep the base's declared
-  position (base's `inferType` prefix priority is authoritative); a genuinely
-  new type — from the child, a `borrow_from`, or a middle pack in the chain —
-  is prepended nearest-first, so a more-derived type's `path_prefix` wins
-  regardless of how deep the chain is.
-- **`takes_kinds` is UNION, not replace** — it carries a Zod default, so an
-  omitted field is indistinguishable from an explicit one. A child can ADD
-  kinds but **cannot narrow** `takes_kinds` below base ∪ parent. If you need a
-  smaller set, don't `extends` a pack that declares the larger one.
-- **`phases` and `calibration_domains` are NOT inherited** (child-only). They
-  gate real cycle execution, so each pack must declare its own participation
-  explicitly — inheriting them would silently make a child run phases it never
-  requested. This is why `gbrain-everything` re-declares all its phases and
-  calibration domains by hand. See `lens-packs.md` for the worked example.
-- **`borrow_from` is selective + non-transitive + fail-closed:** it pulls only
-  the named `types`/`link_types` from the target's OWN declarations (omitting a
-  category borrows none of it); a missing target throws `UnknownPackError`.
-
 ## Recovery + revert
 
 The single-PR cathedral is hard to revert atomically. Per codex finding
@@ -214,7 +186,7 @@ gbrain schema downgrade
 
 1. `git revert <merge-commit>` — restores the code.
 2. `gbrain schema downgrade --to gbrain-base` — restores config.
-3. (Optional) `gbrain purge-deleted --older-than 0h` — drops
+3. (Optional) `gbrain pages purge-deleted --older-than 0h` — drops
    v0.39-typed pages that no longer have a matching type in the active
    pack.
 

docs/architecture/system-of-record.md

@@ -19,13 +19,11 @@ entire DB from scratch.
 
 This means:
 
-- **Disaster recovery is a short, boring sequence.** If your DB volume
-  corrupts, if Postgres eats itself, if PGLite's WASM lock wedges — you
-  don't need a backup. You wipe the derived tables (on PGLite,
-  `gbrain reinit-pglite` wipes the whole embedded DB), re-import from
-  your brain repo with `gbrain sync`, and `gbrain extract all`
-  regenerates the derived state. See "Disaster recovery" below for the
-  exact commands.
+- **Disaster recovery is one command.** If your DB volume corrupts, if
+  Postgres eats itself, if PGLite's WASM lock wedges — you don't need
+  a backup. You wipe the DB, re-import from your brain repo, and the
+  derived state regenerates. v0.32.3 ships `gbrain rebuild
+  --confirm-destructive` as the documented one-liner.
 - **Multi-machine sync is git.** Your brain is a repo. Push from one
   machine, pull from another, and the second machine's DB rebuilds on
   its next sync. No "back up the database" step.
@@ -148,9 +146,11 @@ The promise the rule makes:
 # Snapshot what's there
 gbrain stats > /tmp/before.txt
 
-# Wipe and rebuild — delete the derived tables (pages + content_chunks
-# survive the CASCADE-safe design), then re-derive from the repo.
-# On PGLite, `gbrain reinit-pglite` wipes the whole embedded DB instead.
+# Wipe and rebuild
+gbrain rebuild --confirm-destructive   # v0.32.3 — deletes derived tables
+                                       # (pages + content_chunks survive
+                                       # the CASCADE-safe design)
+                                       # OR manually for v0.32.2:
 psql -c 'DELETE FROM facts; DELETE FROM takes; DELETE FROM links; DELETE FROM timeline_entries;'
 gbrain sync
 gbrain extract all

docs/architecture/type-taxonomy.md

@@ -108,8 +108,8 @@ Every primitive ships with a documented rollback:
 | Operation | Rollback |
 |-----------|----------|
 | Retype | `frontmatter.legacy_type = <original>` preserved on every page (D8). One SQL UPDATE restores types: `UPDATE pages SET type = frontmatter->>'legacy_type' WHERE frontmatter ? 'legacy_type'`. |
-| Page-to-link | Source page soft-deleted with 72h TTL. `gbrain restore <slug>` within 72h. Link row stays harmless if source restored. |
-| Page-to-alias | Source page soft-deleted with 72h TTL. `gbrain restore <slug>` within 72h. Alias row stays harmless (or `DELETE FROM slug_aliases WHERE alias_slug = <slug>` to clean up). |
+| Page-to-link | Source page soft-deleted with 72h TTL. `gbrain pages restore <slug>` within 72h. Link row stays harmless if source restored. |
+| Page-to-alias | Source page soft-deleted with 72h TTL. `gbrain pages restore <slug>` within 72h. Alias row stays harmless (or `DELETE FROM slug_aliases WHERE alias_slug = <slug>` to clean up). |
 | Active-pack flip | `gbrain schema use gbrain-base` reverses the flip. |
 
 ## What if my brain doesn't fit?

docs/ethos/MARKDOWN_SKILLS_AS_RECIPES.md

@@ -183,6 +183,6 @@ This also means the best AI agent setups will be open source by default. Closed,
 
 Software distribution reimagined: the package is a markdown file, the runtime is a sufficiently smart model, the package manager is your AI agent, and the app store is a git repo.
 
-`gbrain skillpack scaffold voice-agent`
+`gbrain install voice-agent`
 
 That's it.

docs/guides/agent-to-gbrain.md

@@ -159,8 +159,7 @@ proxy for worker env.
   If a brain DB ever traverses a trust boundary, secrets stay out.
 - **Free-form names.** `inherit:` accepts any snake_case config-key on your
   worker — `database_url`, `anthropic_api_key`, `openai_api_key`,
-  `openrouter_api_key`, `voyage_api_key`, `groq_api_key`,
-  `zeroentropy_api_key`, or any custom
+  `voyage_api_key`, `groq_api_key`, `zeroentropy_api_key`, or any custom
   field you stuff into `~/.gbrain/config.json`. The agent picks what it
   needs.
 - **`env:` still works** for non-secret values, or for cases where you

docs/guides/compiled-truth.md

@@ -69,7 +69,7 @@ update_brain_page(slug, new_info, source):
   page = gbrain get {slug}
 
   // TIMELINE: always APPEND (never edit existing entries)
-  gbrain timeline-add {slug} {
+  gbrain add_timeline_entry {slug} {
     date: today,
     summary: new_info.summary,
     detail: new_info.detail,

docs/guides/content-media.md

@@ -46,10 +46,10 @@ on user_shares_media(url_or_file):
 
         # Step 4: Extract and cross-reference entities
         for person in transcript.mentioned_people:
-            gbrain link <slug> <person_slug>
-            gbrain link <person_slug> <slug>
-            gbrain timeline-add <person_slug> {date} \
-                "Discussed in {video_title}: {what_was_said}" \
+            gbrain add_link <slug> <person_slug>
+            gbrain add_link <person_slug> <slug>
+            gbrain add_timeline_entry <person_slug> \
+                --entry "Discussed in {video_title}: {what_was_said}" \
                 --source "YouTube: {url}"
 
     # PATTERN 2: Social Media Bundles
@@ -80,8 +80,8 @@ on user_shares_media(url_or_file):
 
         # Extract entities and cross-reference
         for entity in bundle.mentioned_entities:
-            gbrain link <slug> <entity_slug>
-            gbrain link <entity_slug> <slug>
+            gbrain add_link <slug> <entity_slug>
+            gbrain add_link <entity_slug> <slug>
 
     # PATTERN 3: PDFs and Documents
     elif media.type == "pdf" or media.type == "document":
@@ -109,8 +109,8 @@ on user_shares_media(url_or_file):
         """
 
         for entity in document.mentioned_entities:
-            gbrain link <slug> <entity_slug>
-            gbrain link <entity_slug> <slug>
+            gbrain add_link <slug> <entity_slug>
+            gbrain add_link <entity_slug> <slug>
 
     # Always sync after ingestion
     gbrain sync
@@ -127,7 +127,7 @@ on user_shares_media(url_or_file):
 ## How to Verify
 
 1. Ingest a YouTube video. Run `gbrain get media/youtube/{slug}`. Confirm the page has: the agent's analysis (not just a summary), key quotes with speaker attribution, and the full diarized transcript.
-2. Run `gbrain call get_links '{"slug": "media/youtube/{slug}"}'`. Confirm back-links exist to brain pages for every person and company mentioned in the video.
+2. Run `gbrain get_links media/youtube/{slug}`. Confirm back-links exist to brain pages for every person and company mentioned in the video.
 3. Pick a person mentioned in the video. Run `gbrain get <person_slug>`. Confirm their timeline has a new entry referencing the video with specific context.
 4. Ingest a tweet. Confirm the brain page includes the thread context, linked article summaries, and entity cross-references -- not just the tweet text.
 5. Run `gbrain search "{topic_from_video}"`. Confirm the media page appears in search results (verifies the content is indexed and searchable).

docs/guides/embedding-migration.md

@@ -1,138 +0,0 @@
-# Embedding migration — moving a brain to another embedding provider
-
-`gbrain migrate embeddings` re-embeds an entire brain onto a different
-embedding provider/model, safely and resumably. It is the forward path off a
-sunsetting provider (for example ZeroEntropy's hosted API, which shuts down
-2026-09-04 and is the shipped default for brains that never picked a model) —
-but it is provider-agnostic: any configured `provider:model` works as a
-target.
-
-Also reachable as `gbrain retrieval-upgrade` (the name `doctor` and the
-README reference).
-
-## Quick start
-
-```bash
-# Preview the work + cost. Changes nothing.
-gbrain migrate embeddings --to openai:text-embedding-3-small --dry-run
-
-# Run it (interactive confirm shows chunk count + $ estimate first).
-gbrain migrate embeddings --to openai:text-embedding-3-small
-
-# Non-interactive (cron / scripts): --yes is required, else exit 2.
-gbrain migrate embeddings --to voyage:voyage-3-large --yes
-```
-
-`--dim <N>` overrides the target width; it defaults to the provider recipe's
-declared width and is required for recipes that don't declare one (litellm,
-llama-server, and other bring-your-own-model providers).
-
-## What it does, in order
-
-1. **Plan.** Counts every chunk not already in the target embedding space —
-   including chunks on pages with **no recorded embedding signature**
-   (pages embedded before the v108 provenance stamp). Prices the re-embed
-   from the pricing table; unknown providers print "estimate unavailable"
-   instead of a fabricated number.
-2. **Consent gate.** Prints the plan; requires an interactive `y` or `--yes`.
-   Non-TTY without `--yes` refuses with exit 2 (mirrors the `reindex-code`
-   gate in [spend-controls](../operations/spend-controls.md)). Unlike the pure
-   cost gates there, `spend.posture=tokenmax` does **not** bypass this one:
-   posture waives the spend *ceiling*, and this gate also guards a
-   destructive schema rebuild. Under `tokenmax` the dollar figure is marked
-   informational and the confirmation is still asked. `--yes` is the single
-   scripted bypass.
-3. **Live probe.** One tiny embed against the TARGET provider before any
-   mutation — validates the API key, model id, and dimension support in a
-   single call. A bad key fails here, with nothing changed.
-4. **Env-override gate.** Refuses when `GBRAIN_EMBEDDING_MODEL` /
-   `GBRAIN_EMBEDDING_DIMENSIONS` would silently defeat the switch at
-   runtime (the same guard `ze-switch` uses). `--ignore-env-override` for
-   people running deliberate experiments.
-5. **Apply.** When the target width differs from the actual column width,
-   runs the same atomic schema transition `ze-switch` uses, in one
-   transaction. It rebuilds **all three dim-pinned text-embedding-space
-   columns** — `content_chunks.embedding`, `query_cache.embedding`, and
-   `facts.embedding` — at the new width, preserving each column's type
-   (`vector` vs `halfvec`) and recreating its HNSW index. Missing any of the
-   three leaves it silently broken: a narrow `query_cache.embedding` makes
-   every cache write and read fail *by design* (the cache swallows errors so
-   it can never break search) for a permanent 0% hit rate, and a narrow
-   `facts.embedding` fails every per-fact embed write. The image/multimodal
-   columns ARE deliberately untouched — they use separate models whose
-   dimensions are independent of the text embedding model.
-   Writes `embedding_model` + `embedding_dimensions` to BOTH config planes
-   (file plane for the runtime gateway, DB plane for doctor), invalidates
-   every chunk still in the old space — **including NULL-signature pages** —
-   and purges the semantic query cache so stale cached results can't be
-   served across the swap.
-6. **Re-embed.** The standard embed pipeline (`embed --stale --catch-up`)
-   with per-source single-flight locks, rate-limit backoff, stderr progress,
-   and optional DB-contention pacing (`--pace[=mode]`).
-
-## What the rebuild deletes
-
-The dimension change **deletes every stored embedding vector** in the brain —
-they are in the old model's space and unusable. They are not recoverable:
-going back to the previous provider means paying for a second full re-embed.
-`content_chunks` vectors are rebuilt by the re-embed pass, the query cache
-refills on the next query, and fact embeddings are rewritten on their next
-write (or a `gbrain extract` pass).
-
-## Resume after a kill
-
-The NULL-embedding column is the checkpoint. If the run is killed (or some
-pages fail to embed), re-run the **same command**: chunks already embedded on
-the target are never re-embedded, the schema/config steps no-op, and the run
-continues where it stopped. An in-flight marker (`embedding_migration.state`
-in DB config) records the target; it is cleared only when the backlog drains
-to zero.
-
-A page whose chunks straddle two stale batches is embedded correctly but not
-stamped by the embed loop (which only stamps all-or-nothing per batch), so the
-migration runs one reconcile pass after the drain that stamps every
-fully-embedded page. Without it a large brain would report "incomplete" and the
-re-run would pay again for those pages. `--batch-size N` tunes the batch
-(default 2000).
-
-`--no-embed` applies schema + config + invalidation and stops, so you can run
-the (potentially long) re-embed later or in the background:
-
-```bash
-gbrain migrate embeddings --to openai:text-embedding-3-small --yes --no-embed
-gbrain embed --stale --catch-up --include-null-signature --background
-```
-
-## During the migration
-
-While the re-embed runs, semantic search returns degraded (lexical-arm-only)
-results for not-yet-re-embedded content. Pick a quiet window for large
-brains, or use `--pace` to keep the DB responsive.
-
-## Pages without an embedding signature (#3391)
-
-Pages embedded before provenance stamping have `embedding_signature IS NULL`
-and are grandfathered by the routine stale sweep (so an upgrade never
-surprise-re-embeds a whole corpus). After a provider swap that grandfather
-clause would silently leave those pages in the OLD embedding space — mixed
-vector spaces in one index, degrading retrieval with nothing in the logs.
-
-- `gbrain migrate embeddings` always includes them.
-- Plain `gbrain embed --stale` warns when a model swap leaves NULL-signature
-  pages behind, and `gbrain embed --stale --include-null-signature` re-embeds
-  them.
-
-## Reranker
-
-Migrating embeddings does not touch the reranker. If
-`search.reranker.model` points at the outgoing provider, the plan prints a
-warning; disable it (`gbrain config set search.reranker.enabled false`) or
-point it at another provider.
-
-## Self-hosting instead of migrating
-
-If the outgoing model's weights are available (zembed-1's are Apache-2.0),
-serving them locally via `llama-server` / `ollama` / a LiteLLM proxy
-preserves your existing vectors — no re-embed at all. Point
-`embedding_model` at the local recipe and keep the same dimensions. The
-migration command is for when you'd rather move to a hosted provider.

docs/guides/enrichment-pipeline.md

@@ -49,23 +49,23 @@ on enrich(entity, trigger):
         data["contacts"] = google_contacts(entity.email)   # Contact data
 
     # Step 5: Store raw data (auditable, re-processable)
-    gbrain call put_raw_data \
-        '{"slug": "<entity_slug>", "data": {"sources": {"crustdata": {"fetched_at": "...", "data": {...}}, ...}}}'
+    gbrain put_raw_data <entity_slug> \
+        --data '{"sources": {"crustdata": {"fetched_at": "...", "data": {...}}, ...}}'
     # Overwrite on re-enrichment, don't append
 
     # Step 6: Write to brain page
     if path == "CREATE":
         gbrain put <entity_slug> --content "<compiled_truth_from_all_sources>"
-        gbrain timeline-add <entity_slug> {date} "Page created via enrichment"
+        gbrain add_timeline_entry <entity_slug> --entry "Page created via enrichment"
     elif path == "UPDATE":
         # Append timeline, update compiled truth ONLY if materially new
-        gbrain timeline-add <entity_slug> {date} "Enriched: {new_signal}"
+        gbrain add_timeline_entry <entity_slug> --entry "Enriched: {new_signal}"
         # Flag contradictions -- don't silently resolve them
 
     # Step 7: Cross-reference the graph
-    gbrain link <person_slug> <company_slug>       # person -> company
-    gbrain link <company_slug> <person_slug>       # company -> person
-    gbrain link <person_slug> <deal_slug>          # person -> deal
+    gbrain add_link <person_slug> <company_slug>       # person -> company
+    gbrain add_link <company_slug> <person_slug>       # company -> person
+    gbrain add_link <person_slug> <deal_slug>          # person -> deal
     # Every entity page links to every other entity page that references it
 
 # People page sections (not a LinkedIn profile -- a living portrait):
@@ -94,8 +94,8 @@ on enrich(entity, trigger):
 ## How to Verify
 
 1. Enrich a Tier 1 person. Run `gbrain get <slug>` and confirm the page has Executive Summary, State, What They Believe, Contact, and Timeline sections populated from multiple sources.
-2. Run `gbrain call get_raw_data '{"slug": "<slug>"}'`. Confirm raw API responses are stored with `sources.{provider}.fetched_at` timestamps.
-3. Run `gbrain call get_links '{"slug": "<slug>"}'`. Confirm cross-reference links exist to the person's company page, deal pages, and related entities.
+2. Run `gbrain get_raw_data <slug>`. Confirm raw API responses are stored with `sources.{provider}.fetched_at` timestamps.
+3. Run `gbrain get_links <slug>`. Confirm cross-reference links exist to the person's company page, deal pages, and related entities.
 4. Check a page that was enriched AND has a user-written Assessment. Confirm the Assessment section was preserved, not overwritten by API data.
 5. Try to re-enrich the same person. Confirm the system checks the `fetched_at` timestamp and skips if less than a week old.
 

docs/guides/executive-assistant.md

@@ -53,7 +53,7 @@ on upcoming_meeting(meeting):
                 "last_interaction": page.timeline[0],     # most recent
                 "open_threads": page.open_threads,
                 "relationship_temperature": page.relationship,
-                "relevant_deals": gbrain call get_links '{"slug": "<attendee_slug>"}',
+                "relevant_deals": gbrain get_links <attendee_slug>,
             }
         else:
             briefing[attendee] = "No brain page -- consider enriching"
@@ -67,14 +67,14 @@ on inbox_cleared():
     for email in processed_emails:
         if email.contained_new_information:
             # Update the sender's brain page with new signal
-            gbrain timeline-add <sender_slug> {date} \
-                "Email re: {subject}. Key info: {extracted_signal}" \
+            gbrain add_timeline_entry <sender_slug> \
+                --entry "Email re: {subject}. Key info: {extracted_signal}" \
                 --source "email from {sender} re {subject}, {date}"
 
             # Update any mentioned entity pages too
             for entity in email.mentioned_entities:
-                gbrain timeline-add <entity_slug> {date} \
-                    "{what_was_said_about_them}" \
+                gbrain add_timeline_entry <entity_slug> \
+                    --entry "{what_was_said_about_them}" \
                     --source "email from {sender}, {date}"
 
 # WORKFLOW 4: Scheduling Nudges

docs/guides/live-sync.md

@@ -21,17 +21,14 @@ GBrain is tuned for the Supabase **Transaction pooler** (port 6543): it
 auto-disables prepared statements there and routes `engine.transaction()`
 (migrations, DDL, sync imports) to a derived **direct** connection
 (`db.<ref>.supabase.co:5432`). That direct host is IPv6-only, so on an
-IPv4-only host it is unreachable. When that happens gbrain now falls back to
-the pooler automatically (one stderr warning, then single-pool mode for the
-rest of the process) — but the pooler's ~2-min statement timeout can truncate
-very long migrations or bulk imports.
+IPv4-only host, reads work but sync **silently skips most pages**. This is the
+number one cause of "sync ran but nothing happened."
 
 Fix: make the direct connection reachable over IPv4. Either set
 `GBRAIN_DIRECT_DATABASE_URL` to the **Session pooler** string (port 5432 on the
-`pooler.supabase.com` host, IPv4), or enable Supabase's IPv4 add-on.
-`GBRAIN_DISABLE_DIRECT_POOL=1` skips the direct pool (and the fallback warning)
-entirely. Verify by running `gbrain sync` and checking that the page count in
-`gbrain stats` matches the syncable file count in the repo.
+`pooler.supabase.com` host, IPv4), or enable Supabase's IPv4 add-on. Verify by
+running `gbrain sync` and checking that the page count in `gbrain stats` matches
+the syncable file count in the repo.
 
 ### The Primitives
 

docs/guides/meeting-ingestion.md

@@ -32,15 +32,15 @@ on new_meeting_transcript(meeting):
 
     # Step 3: Propagate to ALL entity pages (MANDATORY -- most agents skip this)
     for person in meeting.attendees + meeting.mentioned_people:
-        gbrain timeline-add <person_slug> {date} \
-            "Met in '{meeting.title}' on {date}. Key points: ..." \
+        gbrain add_timeline_entry <person_slug> \
+            --entry "Met in '{meeting.title}' on {date}. Key points: ..." \
             --source "Meeting notes '{meeting.title}', {date}"
         # Update their State section if new information surfaced
         # Update company pages for each person's company if relevant
 
     for company in meeting.mentioned_companies:
-        gbrain timeline-add <company_slug> {date} \
-            "Discussed in '{meeting.title}': {what_was_said}" \
+        gbrain add_timeline_entry <company_slug> \
+            --entry "Discussed in '{meeting.title}': {what_was_said}" \
             --source "Meeting notes '{meeting.title}', {date}"
 
     # Step 4: Extract action items
@@ -49,8 +49,8 @@ on new_meeting_transcript(meeting):
 
     # Step 5: Back-link everything (bidirectional graph)
     for entity in all_entities_mentioned:
-        gbrain link <slug> <entity_slug>   # meeting -> entity
-        gbrain link <entity_slug> <slug>    # entity -> meeting
+        gbrain add_link <slug> <entity_slug>   # meeting -> entity
+        gbrain add_link <entity_slug> <slug>    # entity -> meeting
 
     # Step 6: Sync so new pages are immediately searchable
     gbrain sync
@@ -73,7 +73,7 @@ on new_meeting_transcript(meeting):
 1. After ingesting a meeting, run `gbrain get meetings/{date}-{slug}`. Confirm the page has the agent's analysis above the bar and the full diarized transcript below it.
 2. For each attendee, run `gbrain get <attendee_slug>`. Check that their timeline has a new entry referencing the meeting with specific insights (not just "attended meeting").
 3. Pick a company mentioned in the meeting. Run `gbrain get <company_slug>`. Confirm a timeline entry exists referencing what was discussed about the company.
-4. Run `gbrain call get_links '{"slug": "meetings/{date}-{slug}"}'`. Verify back-links exist to all attendee and entity pages.
+4. Run `gbrain get_links meetings/{date}-{slug}`. Verify back-links exist to all attendee and entity pages.
 5. Run `gbrain search "{meeting_topic}"`. Confirm the meeting page appears in search results (verifies sync ran).
 
 ---

docs/guides/minions-shell-jobs.md

@@ -155,7 +155,6 @@ child-spawn time:
 - `inherit: ["database_url"]` → child env `GBRAIN_DATABASE_URL`
 - `inherit: ["anthropic_api_key"]` → child env `ANTHROPIC_API_KEY`
 - `inherit: ["openai_api_key"]` → child env `OPENAI_API_KEY`
-- `inherit: ["openrouter_api_key"]` → child env `OPENROUTER_API_KEY`
 - `inherit: ["voyage_api_key"]` → child env `VOYAGE_API_KEY`
 - `inherit: ["groq_api_key", "zeroentropy_api_key"]` → both injected
 - Or any arbitrary config-key your worker has (`my_custom_field` →

docs/guides/multi-source-brains.md

@@ -91,7 +91,7 @@ first):
 6. The seeded `default` source.
 
 So inside `~/.gstack/plans/` on a brain that pinned `gstack` to
-`~/.gstack` via `.gbrain-source`, `gbrain put` implicitly writes to
+`~/.gstack` via `.gbrain-source`, `gbrain put-page` implicitly writes to
 the `gstack` source. Outside any registered directory with no env/dotfile
 set, it writes to the default.
 
@@ -188,10 +188,10 @@ citations keep working.
 
 ```bash
 # Pass --source explicitly
-gbrain put topics/ai ... --source wiki
+gbrain put-page topics/ai ... --source wiki
 
 # Or rely on the dotfile / env / CWD match
-cd ~/.gstack && gbrain put plans/multi-repo ...
+cd ~/.gstack && gbrain put-page plans/multi-repo ...
 # → source auto-resolves to gstack
 ```
 

docs/guides/operational-disciplines.md

@@ -20,8 +20,8 @@ on every_inbound_message(message):
     for entity in entities:
         existing = gbrain search "{entity.name}"
         if existing:
-            gbrain timeline-add <entity_slug> {date} \
-                "{what_was_said}" \
+            gbrain add_timeline_entry <entity_slug> \
+                --entry "{what_was_said}" \
                 --source "User, direct message, {timestamp}"
         # else: flag for enrichment if important enough
 
@@ -64,13 +64,13 @@ on nightly_schedule("02:00"):
     # The brain COMPOUNDS overnight.
 
     # 5a: Entity sweep -- find unlinked mentions
-    pages = gbrain list
+    pages = gbrain list_pages
     for page in pages:
         mentions = extract_entity_mentions(page.content)
-        existing_links = gbrain call get_links '{"slug": "<page.slug>"}'
+        existing_links = gbrain get_links <page.slug>
         for mention in mentions:
             if mention not in existing_links:
-                gbrain link <page.slug> <mention_slug>  # fix broken graph
+                gbrain add_link <page.slug> <mention_slug>  # fix broken graph
 
     # 5b: Citation audit -- find facts without sources
     for page in pages:
@@ -80,7 +80,7 @@ on nightly_schedule("02:00"):
 
     # 5c: Memory consolidation -- update compiled truth from timeline
     for page in stale_pages(older_than="7d"):
-        timeline = gbrain timeline <page.slug>
+        timeline = gbrain get_timeline <page.slug>
         if timeline.has_new_entries_since_last_consolidation:
             # Re-synthesize compiled truth from accumulated timeline
             updated_truth = consolidate(page.compiled_truth, timeline.new_entries)
@@ -110,11 +110,11 @@ on nightly_schedule("02:00"):
 
 ## How to Verify
 
-1. Send a message mentioning a person with a brain page. Confirm the agent detects the entity and adds a timeline entry to their page (`gbrain timeline <slug>`).
+1. Send a message mentioning a person with a brain page. Confirm the agent detects the entity and adds a timeline entry to their page (`gbrain get_timeline <slug>`).
 2. Ask the agent about someone in the brain. Confirm it runs `gbrain search` or `gbrain get` BEFORE reaching for external APIs (check the tool call order).
 3. Write a new page with `gbrain put`, then immediately run `gbrain search` for it. Confirm it appears in results (verifies sync ran).
 4. Run `gbrain doctor`. Confirm it returns a health report with database status, page count, and any flagged issues.
-5. After a dream cycle runs, check a page that had unlinked entity mentions. Confirm new links were added (`gbrain call get_links '{"slug": "<slug>"}'`).
+5. After a dream cycle runs, check a page that had unlinked entity mentions. Confirm new links were added (`gbrain get_links <slug>`).
 
 ---
 *Part of the [GBrain Skillpack](../GBRAIN_SKILLPACK.md).*

docs/guides/originals-folder.md

@@ -47,8 +47,8 @@ on user_message(message):
 
         # Step 3: Cross-link to everything that shaped the thinking
         for entity in idea.influences:
-            gbrain link originals/{slug} <entity_slug>
-            gbrain link <entity_slug> originals/{slug}
+            gbrain add_link originals/{slug} <entity_slug>
+            gbrain add_link <entity_slug> originals/{slug}
 
         # Step 4: Sync
         gbrain sync
@@ -79,7 +79,7 @@ on user_message(message):
 
 1. Generate an original idea in conversation (e.g., "I call this the 'ambition debt' problem -- every year you delay going big, the compound interest works against you"). Confirm a new page appears at `brain/originals/ambition-debt` with `gbrain get originals/ambition-debt`.
 2. Check that the page uses the user's exact phrasing for the title and slug -- not a sanitized version.
-3. Run `gbrain call get_links '{"slug": "originals/ambition-debt"}'`. Confirm cross-links exist to related people, meetings, or other originals.
+3. Run `gbrain get_links originals/ambition-debt`. Confirm cross-links exist to related people, meetings, or other originals.
 4. Express a take on someone else's idea (e.g., "I think Thiel's contrarian question is wrong because..."). Confirm it goes to `originals/` (synthesis is original), not `concepts/`.
 5. Run `gbrain search "ambition debt"`. Confirm the originals page appears in search results and is discoverable.
 

docs/guides/plugin-authors.md

@@ -87,7 +87,7 @@ expect it.
 | `version`        | string | yes      | Your plugin's semver. Informational.                               |
 | `plugin_version` | string | yes      | Contract lock. Must equal `"gbrain-plugin-v1"` for v0.15.          |
 | `subagents`      | string | no       | Subdir name (default `subagents`). Escape-attempts are rejected.   |
-| `description`    | string | no       | Shown in a future plugin-listing command.                          |
+| `description`    | string | no       | Shown in future `gbrain plugin list`.                              |
 
 ## Subagent definition files
 

docs/guides/skillpacks-as-scaffolding.md

@@ -131,9 +131,7 @@ into gbrain so other clients can scaffold it. Default behavior:
   `~/.gbrain/harvest-private-patterns.txt` plus built-in defaults
   (canonical private fork name, common email regex, Slack channel pattern). Any
   match → rollback (delete the harvested files) and exit non-zero.
-- `openclaw.plugin.json` updated with the new slug, sorted. Harvest must preserve
-  the top-level OpenClaw-native plugin fields (`id`, `configSchema`, `contracts`)
-  because OpenClaw validates those before it can install the package.
+- `openclaw.plugin.json` updated with the new slug, sorted.
 - `--no-lint` bypasses the linter (after a manual editorial scrub).
 
 Use the `skillpack-harvest` skill (its companion editorial workflow)

docs/integrations/embedding-providers.md

@@ -103,7 +103,7 @@ For GCP service-account / Vertex AI auth (production deployments), see the v0.32
 
 ### OpenRouter
 
-Single OpenAI-compatible API for fan-out to OpenAI, Anthropic, Google, DeepSeek, Meta Llama, Qwen, and dozens of other hosted providers. One key, many models. Set `OPENROUTER_API_KEY` or `openrouter_api_key` in `~/.gbrain/config.json`, then use `openrouter:<provider>/<model>` (e.g. `openrouter:openai/gpt-5.2`, `openrouter:anthropic/claude-sonnet-4.6`).
+Single OpenAI-compatible API for fan-out to OpenAI, Anthropic, Google, DeepSeek, Meta Llama, Qwen, and dozens of other hosted providers. One key, many models. Set `OPENROUTER_API_KEY` and use `openrouter:<provider>/<model>` (e.g. `openrouter:openai/gpt-5.2`, `openrouter:anthropic/claude-sonnet-4.6`).
 
 **Embedding**: `openai/text-embedding-3-small` (1536d default, Matryoshka shrink to 512/768/1024). OR's embedding catalog also includes `text-embedding-3-large`, `google/gemini-embedding-2-preview`, `qwen/qwen3-embedding-8b`, `bge-m3` — opt in via `--embedding-model openrouter:<id>`. Pricing matches the upstream provider (OR adds a small markup).
 

docs/mcp/DEPLOY.md

@@ -250,7 +250,7 @@ All 30 GBrain operations are available remotely, including `sync_brain` and
 directory where `gbrain serve` was launched. Symlinks, `..` traversal, and absolute
 paths outside cwd are rejected. Page slugs and filenames are allowlist-validated
 (alphanumeric + hyphens; no control chars, RTL overrides, or backslashes). Local
-CLI callers (`gbrain files upload ...`) keep unrestricted filesystem access since
+CLI callers (`gbrain file upload ...`) keep unrestricted filesystem access since
 the user owns the machine.
 
 ## Deployment Options
@@ -258,43 +258,6 @@ the user owns the machine.
 See [ALTERNATIVES.md](ALTERNATIVES.md) for a comparison of ngrok, Tailscale
 Funnel, and cloud hosts (Fly.io, Railway).
 
-### Co-located Docker workloads (self-hosted Postgres)
-
-OAuth scopes and source scoping guard the `gbrain serve --http` path. They do
-NOT guard raw Postgres. If the brain's Postgres runs as a container on the same
-Docker host as other workloads (agent runtimes, n8n, staging fixtures), any
-container sharing Docker's default `bridge` network can open a direct DB
-session — no OAuth token required — and read every source. That silently
-recreates a privileged path underneath the isolation you configured at the MCP
-layer.
-
-Network-zone the host so untrusted containers can never reach Postgres:
-
-```
-Docker host
-├── gbrain-net          ← ONLY the brain's Postgres (+ gbrain serve, if containerized)
-├── agent-<id>-net      ← each untrusted agent runtime, isolated
-└── default bridge      ← no secret-bearing databases
-```
-
-Operator checklist:
-
-```text
-[ ] Postgres is on a user-defined Docker network, not the default bridge
-    (or nothing else runs on that bridge)
-[ ] If Postgres publishes a host port at all, it binds loopback only
-    (`-p 127.0.0.1:5432:5432`, never `0.0.0.0`)
-[ ] Untrusted agent containers have no DATABASE_URL or Postgres password
-[ ] Untrusted agents reach the brain via OAuth/Bearer against serve --http only
-    (host loopback via host.docker.internal / host gateway — never gbrain-net)
-[ ] OAuth clients are least-privilege: scoped --source / --federated-read,
-    pre-minted short-lived tokens preferred over long-lived client secrets
-[ ] Isolation verified: a team-scoped client cannot read internal-only sources
-```
-
-Optional defense-in-depth: a dedicated Postgres role (or RLS) limited to the
-allowed `source_id`s, so even a leaked connection string can't read everything.
-
 ## Troubleshooting
 
 **"missing_auth" error**

docs/operations/conversation-backfill-outcomes.md

@@ -1,227 +0,0 @@
-# Conversation backfill durable outcomes
-
-`gbrain extract-conversation-facts` stores page-level outcomes in `facts` so
-bulk runs, autopilot, and `gbrain doctor` can distinguish finished work from
-retryable work without adding another state table.
-
-This is completion authority, not ordinary extracted knowledge. The authority
-is deliberately narrow: a marker is valid only for the exact page or transcript
-snapshot that was parsed, and only after every required operation succeeded.
-
-## Outcome protocol
-
-The current protocol is v2. Its source names are versioned so rows written by
-older best-effort implementations cannot suppress a corrective replay.
-
-| Outcome | `facts.source` | Meaning |
-|---|---|---|
-| Complete | `cli:extract-conversation-facts:terminal:v2` | Every eligible segment was extracted and inserted successfully, the input remained unchanged, and the terminal write succeeded. |
-| Scanned, not extractable | `cli:extract-conversation-facts:non-extractable:v2` | A recognized input was scanned successfully but contained no eligible multi-message segment. |
-| Unfinished | no matching v2 outcome | Work is pending, failed, was not recognized, changed during extraction, or has only a legacy marker. |
-
-The non-extractable outcome is intentionally separate from completion. It does
-not claim that knowledge facts were extracted. CLI counters, cycle details, and
-doctor output preserve that distinction.
-
-## Snapshot identity
-
-Every v2 marker binds `source_session` to the parser input snapshot:
-
-```text
-<outcome-source>:<page-slug>:<version-token>
-```
-
-There are two token forms.
-
-### Database-backed page body
-
-For pages parsed from `compiled_truth` and `timeline`, the token is:
-
-```text
-page-<pages.content_hash>-<effective-date>
-```
-
-`content_hash` covers title, type, compiled truth, timeline, and frontmatter.
-The effective-date suffix covers the remaining date input used by parsing. This
-identity does not depend on JavaScript's millisecond timestamp precision, so two
-writes within one PostgreSQL millisecond still produce different tokens when
-parser input changes. A legacy page with a null content hash uses a computed
-SHA-256 fallback and is verified in-process by both extraction and doctor.
-
-### Raw transcript sidecar
-
-When frontmatter contains `raw_transcript`, the source text lives outside the
-page row and may change without changing `pages.updated_at`. Its token is:
-
-```text
-sidecar-<SHA-256>
-```
-
-The digest covers the exact body given to the parser plus parser-relevant page
-metadata: title, type, frontmatter, and effective date. Selection recomputes
-the digest before skipping work. A sidecar-only edit therefore reopens the page.
-
-`gbrain doctor` cannot read sidecars in its SQL aggregate, so it enumerates those
-pages in bounded batches and calls the same canonical verifier used by
-extraction. Doctor and extraction therefore agree after sidecar-only edits.
-
-## Selection and locking
-
-Bulk extraction follows this sequence:
-
-1. Enumerate candidate pages in bounded batches.
-2. Filter candidates with matching v2 outcomes.
-3. Apply `--limit` to the remaining pages that actually need work.
-4. Acquire the source-and-slug advisory lock.
-5. Re-fetch the page under that lock.
-6. Recompute and recheck the snapshot-bound outcome.
-7. Prepare one immutable parser snapshot and process it.
-8. Re-fetch and recompute the snapshot before writing an outcome.
-
-The pre-lock check avoids parser, filesystem, and model work for ordinary
-completed pages. The under-lock refetch prevents a stale enumeration object
-from becoming the certified input. The final comparison prevents an edit that
-happens during model or insertion work from receiving a marker for old content.
-
-An edit can occur after the final comparison and before marker insertion. That
-is still safe because the marker contains the old version token. Future
-selection compares the token, not marker creation time, and reopens the page.
-
-Single-page `--slug` runs use the same under-lock path.
-
-## Strict extraction success
-
-The general `extractFactsFromTurn` API remains best-effort for interactive
-callers. It historically returns an empty array for both a legitimate zero-fact
-answer and several model failures.
-
-Conversation backfill instead uses `extractFactsFromTurnWithOutcome`, whose
-result separates:
-
-- `{ ok: true, facts: [] }`, a successful extraction with no durable facts;
-- `{ ok: true, facts: [...] }`, a successful extraction with facts; and
-- `{ ok: false, reason, error? }`, an unavailable provider, provider error,
-  refusal, content filter, malformed output, or repeated truncation.
-
-Any failed segment aborts the page attempt. Any `insertFacts` failure also
-aborts it. The page receives neither a checkpoint advancement nor a terminal
-outcome. Facts inserted by earlier segments may remain temporarily, but the
-next claim deletes this command's rows for the page and replays cleanly.
-
-Bulk workers continue past an individual page failure, but they do not hide it.
-`pages_failed` counts failed claims, stderr names each page, the CLI exits 1,
-the autopilot phase reports `warn`, and receipts/rollups classify the run as
-incomplete. A tolerant pool is therefore observable without sacrificing the
-rest of a large backfill.
-
-This distinction is load-bearing. Treating a provider outage as a successful
-zero-fact response would make a transient failure durable and permanently hide
-the page from later runs.
-
-## Non-extractable authority
-
-A non-extractable marker is written only when all of the following are true:
-
-- a deterministic or accepted parser format recognized the input;
-- ordinary segmentation produced no eligible multi-message segment;
-- the parser phase was not `no_match`;
-- cleanup of prior command-owned rows succeeded; and
-- the input snapshot was still current immediately before cleanup and write.
-
-A `no_match` result stays unfinished so a new parser pattern, optional fallback,
-or corrected input can recover it. Oversize pages, disappeared pages, lock
-contention, dry runs, aborts, cleanup errors, provider failures, extraction
-failures, insertion failures, and outcome-write failures also stay unfinished.
-
-Cleanup errors are never interpreted as "zero rows deleted." Propagating them
-prevents a fresh non-extractable marker from coexisting with stale extracted
-facts that could not be removed.
-
-## Checkpoints are not authority
-
-Operation checkpoints are only progress hints. They do not prove which page
-snapshot was processed, and old checkpoint entries do not include a snapshot
-token. When a page lacks a matching v2 outcome, the command discards that
-page's checkpoint entry and performs a delete-first full replay.
-
-This rule prevents two corruption classes:
-
-- edited text with timestamps older than the old watermark being skipped; and
-- command-owned facts being deleted while the checkpoint skips the segments
-  needed to recreate them.
-
-Deleting `op_checkpoints` does not reopen pages with matching v2 outcomes.
-Deleting or editing an outcome does not make a checkpoint authoritative.
-
-## `--limit` semantics
-
-`--limit N` caps pages that require processing, not completed pages inspected
-while finding them. Durable filtering happens before clipping a batch. With a
-completed page first and a pending page second, `--limit 1` processes the
-pending page rather than consuming the limit on the completed page.
-
-`pages_considered` may therefore exceed `--limit` because it includes durable
-outcomes observed during selection. Model-bearing page work does not exceed the
-limit.
-
-## `--force`
-
-`--force` bypasses durable outcome selection and clears the page checkpoint.
-It still uses delete-first replay, strict extraction outcomes, advisory locks,
-and snapshot verification. Force means "recompute" rather than "relax safety."
-
-## Operator signals
-
-The result exposes separate counters:
-
-- `pages_skipped_completed`
-- `pages_skipped_non_extractable`
-- `pages_marked_non_extractable`
-- `pages_failed`
-
-The CLI aggregates these across sources. The autopilot backfill phase includes
-them in phase details. `gbrain doctor` reports `completed`,
-`scanned_not_extractable`, and `backlog` independently.
-
-Run a small canary twice:
-
-```bash
-gbrain extract-conversation-facts --source-id default --limit 10 --workers 1 --max-cost-usd 0.25 --yes
-gbrain extract-conversation-facts --source-id default --limit 10 --workers 1 --max-cost-usd 0.25 --yes
-gbrain doctor
-```
-
-On the second run, unchanged pages should move through durable skip counters.
-Edit one page or raw transcript sidecar and rerun; that page should process
-again and receive a marker with a new token.
-
-## Maintainer contracts
-
-- Version completion protocols when their success guarantees change.
-- Require an exact `source`, page slug, and snapshot-bound `source_session`.
-- Keep completion and non-extractable as different sources and counters.
-- Re-fetch after acquiring the lock; never certify the enumeration object.
-- Revalidate the snapshot before writing either durable outcome.
-- Keep sidecar content in the version identity.
-- Keep regular-page content hash and effective date in the version identity.
-- Never turn model, insertion, cleanup, cancellation, or parser failures into
-  successful empty extraction.
-- Never classify `no_match` or dry-run output as a durable negative.
-- Do not make operation checkpoints completion authority.
-- Apply work limits after durable filtering.
-- Keep doctor source-scoped by both page and fact `source_id`.
-- Give terminal completion precedence if both current outcome rows exist.
-- Update CLI and cycle aggregation whenever a result counter changes.
-
-## Focused verification
-
-```bash
-bun test test/extract-conversation-facts.test.ts
-bun test test/doctor-conversation-facts-backlog.test.ts
-bun x tsc --noEmit
-```
-
-The focused suite covers checkpoint garbage collection, same-timestamp edits,
-edits during extraction, sidecar-only edits, legacy marker replay, provider and
-insert failures, cleanup failure, recognized non-extractable scans, retryable
-parser misses, post-filter limits, force replay, and doctor accounting.

docs/operations/conversation-parser-llm-fallback.md

@@ -1,240 +0,0 @@
-# Conversation parser LLM fallback
-
-The conversation parser has two stages:
-
-1. A deterministic registry recognizes known transcript formats.
-2. An optional LLM fallback parses pages that every built-in pattern rejects.
-
-The second stage is disabled by default. Enabling it is a privacy decision
-because unmatched transcript text can be sent to the configured utility-tier
-model provider.
-
-## Enable or disable the fallback
-
-Enable it for the current brain:
-
-```bash
-gbrain config set conversation_parser.llm_fallback_enabled true
-```
-
-Disable it:
-
-```bash
-gbrain config set conversation_parser.llm_fallback_enabled false
-```
-
-The key is registered explicitly, so neither command needs `--force`.
-Values other than the exact string `true` leave the fallback disabled.
-
-The setting affects conversation fact extraction. It does not make the
-synchronous `conversation-parser scan` command call a model, and it does not
-enable the separate LLM polish scaffold.
-
-## Select the utility model and run a canary
-
-Inspect the model routing before enabling a production run:
-
-```bash
-gbrain models
-```
-
-The fallback uses the resolved `utility` tier. Override that tier when the
-brain should use a different configured provider or model:
-
-```bash
-gbrain config set models.tier.utility <provider:model>
-```
-
-Start with one known unmatched page and an explicit cost cap:
-
-```bash
-gbrain extract-conversation-facts \
-  --source-id <source-id> \
-  --slug <conversation-slug> \
-  --max-cost-usd 1
-```
-
-Do not add `--dry-run` to this canary. Dry runs deliberately stop before the
-fallback boundary, so they cannot prove provider routing or model output.
-Success emits the per-page fallback log described under
-[Operator visibility](#operator-visibility). After the canary, remove `--slug`
-to process the source normally.
-
-## When the fallback runs
-
-For each eligible conversation page, extraction:
-
-1. Reads the same body used by the deterministic parser, including a configured
-   raw transcript sidecar for meeting pages.
-2. Calls `parseConversation(body, { page })`.
-3. Uses the deterministic messages when any built-in pattern succeeds.
-4. Calls the LLM fallback only when the parse phase is exactly `no_match`, the
-   message list is empty, the opt-in key is `true`, and this is not a dry run.
-5. Splits accepted fallback messages into the normal extraction segments.
-
-The fallback never replaces, edits, or polishes a successful deterministic
-parse. Adding a built-in pattern therefore removes model use for that format
-without changing configuration.
-
-Dry runs remain local and cost-free. They report deterministic segmentation
-only and never send unmatched content to a provider.
-
-## Data sent to the model
-
-The full unmatched body is processed in overlapping windows of at most 100
-non-empty lines, with up to 20 lines of preceding context. Blank lines are
-omitted. Every model request receives:
-
-- an instruction to treat the transcript as untrusted data;
-- an authoritative page date when one can be derived;
-- the sampled transcript inside an explicit chat-log envelope.
-
-The system prompt tells the model not to follow commands or instructions found
-inside transcript content. It asks for message extraction only.
-
-Each window is cached independently. Overlap results with the same normalized
-speaker and timestamp are deduplicated; when one body contains the other, the
-longer body wins. This preserves common multi-line messages that straddle a
-window boundary. If any later window has an ordinary provider or parse failure,
-the fallback returns no page result and extraction does not advance the
-checkpoint. Successful earlier windows stay cached for the retry.
-
-Fallback calls allow up to 8,000 output tokens. Any non-terminal model stop,
-including length truncation, refusal, content filtering, tool use, or an
-unrecognized provider stop, is rejected before parsing and caching. A
-syntactically valid partial JSON array therefore cannot advance a checkpoint.
-
-The utility model is resolved once per source run through the normal model
-configuration chain. The default fallback is the utility-tier Anthropic model.
-
-## Date and timestamp behavior
-
-The fallback uses the deterministic parser's date precedence:
-
-1. an explicit caller date;
-2. `frontmatter.date`;
-3. the page effective date;
-4. `1970-01-01` when no date is known.
-
-A real page date is included in both the prompt and the content-hash cache key.
-Two pages with identical time-only transcript text but different dates cannot
-share a cached parse.
-
-Returned timestamps must be strict RFC3339 date-times with seconds and an
-explicit `Z` or numeric timezone offset. Calendar fields are validated before
-parsing. Accepted timestamps are normalized to whole-second UTC form:
-
-```text
-YYYY-MM-DDTHH:MM:SSZ
-```
-
-Date-only values, timezone-less values, impossible calendar dates, timestamps
-more than 24 hours in the future, blank speakers, and blank message bodies are
-discarded. Valid messages are stable-sorted by timestamp before segmentation.
-Canonical chronological UTC output keeps segment filtering and durable
-checkpoint comparisons stable and prevents future checkpoint poisoning.
-
-If no page date is known, the prompt retains the historical epoch fallback.
-Full timestamps present in the transcript can still be extracted normally.
-
-## Non-chat and failure behavior
-
-The model is instructed to return an empty JSON array for non-chat content.
-An empty response, malformed JSON, unavailable provider, or transport failure
-leaves the page with no messages. Extraction skips that page and continues.
-
-The fallback is fail-open with respect to parser availability. It does not turn
-a model outage into a deterministic-parser outage.
-
-Cancellation and `BudgetExhausted` are control-flow signals, not provider
-failures. The extraction caller explicitly propagates them through the
-fail-open boundary so aborts stay prompt and hard cost caps remain effective.
-An `AbortError` from a provider timeout still fails open while the caller's own
-abort signal remains live.
-
-The gateway can discover an underestimated budget overage only after the final
-provider result. Extraction checks tracker spend against its cap after the run,
-so an overage remains visible even when there is no next model reservation.
-
-## Cache and repeat runs
-
-Successful fallback results use the shared conversation-parser cache:
-
-- an in-process map for repeat calls during one process;
-- the `conversation_parser_llm_cache` table for repeat calls across processes.
-
-Each chunk's cache key includes the call shape, resolved model, page date
-metadata, and chunk content hash. A cached response is still validated before
-it originally enters the cache.
-
-Once fallback messages produce extractable segments, the ordinary per-page
-checkpoint advances to the newest segment timestamp. A later run can read the
-cached parse, apply the checkpoint watermark, and skip already completed
-segments without another provider call.
-
-## Operator visibility
-
-`ExtractConversationFactsResult.pages_llm_fallback` counts pages for which the
-fallback returned at least one valid message. The command also logs:
-
-```text
-[extract-conversation-facts] LLM fallback parsed N message(s) for <slug>
-```
-
-The multi-source CLI summary reports the total number of fallback-parsed pages.
-A zero count means either the fallback was disabled, deterministic patterns
-handled every page, or fallback attempts returned no valid messages.
-
-## Maintainer contracts
-
-Keep these boundaries intact when changing the fallback:
-
-- Default off. Page text must not reach the fallback without the exact opt-in.
-- Never call the provider during `--dry-run`.
-- Deterministic first. Invoke it only for phase `no_match`.
-- One model resolution per source run, not per page.
-- Use `deriveDateContext({ page })` so regex and LLM timestamps share metadata.
-- Put date metadata in the hashed request content to prevent cross-date cache
-  collisions.
-- Process every non-empty line in bounded cached overlapping windows. Preserve
-  common cross-boundary continuations through overlap and deterministic
-  deduplication. Never checkpoint a partial page after a later window fails or
-  returns a non-terminal stop reason.
-- Validate and canonicalize all model-produced fields before segmentation.
-- Stable-sort accepted messages before segmenting or checkpointing them.
-- Keep the exact config key in `KNOWN_CONFIG_KEYS`. Do not register the whole
-  `conversation_parser.*` namespace while other scaffolded keys remain unwired.
-- Preserve `[]` and `null` as skip-page outcomes.
-- Propagate cancellation and budget-stop errors selected by the extraction
-  caller; fail open only for ordinary provider and parse failures.
-- Never persist inferred regexes or promote model guesses into the built-in
-  registry.
-
-## Test coverage
-
-The focused tests cover:
-
-- default-off behavior with zero fallback calls;
-- enabled dry-run behavior with zero provider calls;
-- exact config-key registration;
-- a successful production-path fallback;
-- page-date prompt and cache-key separation;
-- durable checkpoint advancement and cache reuse;
-- complete processing beyond the first 100 non-empty lines;
-- cross-boundary continuation preservation and overlap deduplication;
-- rejection of truncated, refused, and content-filtered model results;
-- all-or-nothing page results when a later chunk fails;
-- non-chat empty arrays and malformed output;
-- strict timestamp normalization, ordering, and invalid-item filtering;
-- provider-unavailable and transport-failure behavior;
-- provider-timeout versus caller-cancellation behavior;
-- thrown and post-record budget-stop reporting.
-
-Run the focused surface with:
-
-```bash
-bun test test/conversation-parser/llm-base.test.ts \
-  test/conversation-parser/llm-fallback.test.ts \
-  test/extract-conversation-facts.test.ts \
-  test/config-set.test.ts
-```

docs/operations/spend-controls.md

@@ -49,7 +49,6 @@ The USD-limit knobs accept `off`, `unlimited`, or `none` (case-insensitive) to m
 | Backfill per-job budget | `embed.backfill_max_usd` | `10` | caps the job's tracker | `off` (`0` → default) | uncapped (still ledgered) |
 | Backfill cooldown | `embed.backfill_cooldown_min` | `10` | skips re-submission inside window | — (latency knob, not spend) | **not** bypassed |
 | `reindex-code` cost gate | — (preview before re-embed) | — | TTY prompt / non-TTY refuse + exit 2 | `--max-cost off` | informational |
-| `migrate embeddings` consent gate | — (plan + estimate before provider migration) | — | TTY y/N prompt / non-TTY refuse + exit 2 | `--yes` | estimate marked informational, but **still prompts** (guards a destructive schema rebuild, not just spend) |
 | `enrich` / `onboard --auto` | `--max-usd` (per-call) | — | refuse without a cap (non-TTY) | `--max-usd off` | runs uncapped (still ledgered) |
 
 ### Sync inline-embed cost gate

docs/progress-events.md

@@ -140,9 +140,6 @@ Stable phase names shipped in v0.15.2:
 - `import.files`
 - `sync.deletes`, `sync.renames`, `sync.imports`
 - `migrate.copy_pages`, `migrate.copy_links`
-- `migrate.reembed` (the re-embed pass of `gbrain migrate embeddings`; total is the
-  stale-chunk backlog at the start of the pass, so it can grow slightly if a
-  writer adds chunks mid-run)
 - `repair_jsonb.run`, `repair_jsonb.<table>.<column>`
 - `backlinks.scan`
 - `lint.pages`

docs/takes-vs-facts.md

@@ -91,18 +91,3 @@ First full takes extraction run on a ~100K-page brain:
 4. **Self-reported ≠ verified.** "Reports 7 figures" → holder=person, weight=0.75, NOT world/1.0
 5. **No false precision.** Use 0.05 increments (0.35, 0.55, 0.75), not 0.74 or 0.82
 6. **"So what" test.** Skip Twitter handles, follower counts, obvious metadata
-
-## Owner-holder canonicalization
-
-"The brain owner" is, by convention, the holder string **`self`** — the value the
-dream `consolidate` phase stamps when it promotes the owner's hot facts into cold
-takes. Calibration, `think`, and the `doctor` calibration check resolve the owner
-holder through `resolveOwnerHolder` (`src/core/owner-holder.ts`): explicit override
-> `emotional_weight.user_holder` config > `self`.
-
-Known limitation (tracked in garrytan/gbrain#2465): the owner can also
-appear under `brain` (a take the owner asserts, via `propose_takes`) and
-`people/<owner>` (extraction that names the owner). The resolver selects the
-*default* canonical owner string for reads; it does not merge those other
-strings. Per-take attribution for other people (e.g. `people/george`) is
-unaffected and correct.

docs/tutorials/README.md

@@ -13,7 +13,7 @@ Step-by-step walkthroughs that take you from zero to a working outcome. Concrete
 
 These are the next tutorials on the roadmap. Open an issue if one of them is the one you need most; that's how we'll prioritize.
 
-- **Set up GBrain for VC dealflow** — the operator's recipe. People pages for founders, companies with typed Facts fence carrying ARR / team-size / runway across dates, meetings auto-ingested, deal pages linking everything. Shows `gbrain whoknows`, `gbrain find-trajectory`, and `gbrain founder scorecard` on real workflows.
+- **Set up GBrain for VC dealflow** — the operator's recipe. People pages for founders, companies with typed Facts fence carrying ARR / team-size / runway across dates, meetings auto-ingested, deal pages linking everything. Shows `gbrain whoknows`, `gbrain find_trajectory`, and `gbrain founder scorecard` on real workflows.
 
 - **Migrate your existing vault into GBrain** — for Notion / Obsidian / Roam users with a vault that doesn't match GBrain's default layout. Walks through `gbrain schema detect` → `suggest` → `review-candidates` so the brain learns your shape instead of forcing you to learn its.
 

docs/tutorials/company-brain.md

@@ -484,10 +484,6 @@ Returns a per-source dashboard: when each source last synced, how many pages, ho
 
 The admin dashboard at `https://brain.acme-co.com/admin` shows live request volume, registered OAuth clients, recent activity, and brain stats. Use the admin bootstrap token from Part 4 to log in the first time, then register additional admin users from inside the dashboard.
 
-### If agents run as containers on the same Docker host
-
-OAuth source scoping only guards the HTTP MCP path. If the brain's Postgres and your teammates' agent runtimes are containers on the same Docker host, make sure the agents can't reach Postgres directly over Docker's default bridge network — a direct DB session skips OAuth entirely. Put Postgres on its own user-defined network, publish it loopback-only if at all, and never hand agent containers a `DATABASE_URL`. The copy-paste operator checklist lives in [docs/mcp/DEPLOY.md — Co-located Docker workloads](../mcp/DEPLOY.md#co-located-docker-workloads-self-hosted-postgres).
-
 ---
 
 ## Part 13: Cost and speed expectations
@@ -554,7 +550,7 @@ What to do next:
 
 - **Wire ingestion** from external systems (Granola, Linear, Slack) using the [ingestion source contract](../skillpack-anatomy.md). Most companies want their meetings auto-ingested so the brain stays current without anyone typing notes.
 - **Set up team-specific dashboards** through the admin UI. Each team lead can have their own view of brain health and activity.
-- **Explore the rest of the brain layer.** `gbrain whoknows` (find the expert on a topic), `gbrain find-trajectory` (how a metric changed over time), `gbrain founder scorecard` (especially useful for VC and ops teams), the contradiction-detection cycle that surfaces conflicts between different people's notes.
+- **Explore the rest of the brain layer.** `gbrain whoknows` (find the expert on a topic), `gbrain find_trajectory` (how a metric changed over time), `gbrain founder scorecard` (especially useful for VC and ops teams), the contradiction-detection cycle that surfaces conflicts between different people's notes.
 
 If you're building in this space (which YC has flagged as the [company-brain category in its Request for Startups](https://www.ycombinator.com/rfs#company-brain)), you might as well build on this. Everything described above is open source, MIT licensed, and what I run in production behind my own AI agents.
 

docs/tutorials/improving-skills-with-skillopt.md

@@ -233,14 +233,13 @@ keep it or `git checkout` to throw it away. Nothing is committed for you.
 
 **For a skill that ships with gbrain** (anything under the gbrain repo's own
 `skills/`): SkillOpt refuses to overwrite it by default and writes the winner to
-`skills/<name>/skillopt/proposed.md` instead (while keeping `best.md` as the
-optimizer's current-best pointer), so an optimization pass can never silently
-mutate a skill other people depend on. Two ways to handle that:
+`skills/<name>/skillopt/best.md` instead, so an optimization pass can never
+silently mutate a skill other people depend on. Two ways to handle that:
 
 ```bash
 # See the proposed improvement without touching SKILL.md (works for ANY skill):
 gbrain skillopt meeting-prep --split 1:1:1 --no-mutate
-# → writes skills/meeting-prep/skillopt/proposed.md, updates best.md, and prints the proposal path.
+# → writes skills/meeting-prep/skillopt/best.md (the proposed rewrite), prints its path. Copy what you want.
 
 # Actually rewrite a bundled skill (explicit opt-in + an independent held-out set):
 gbrain skillopt brain-ops --split 1:1:1 --allow-mutate-bundled \

docs/tutorials/personal-brain.md

@@ -115,21 +115,21 @@ You can use the same keys across multiple agents.
 
 ## Step 6: Install GBrain
 
-Once OpenClaw is running, installation is two commands — one in the brain repo, one in the agent workspace:
+Once OpenClaw is running:
 
 ```bash
-# In the BRAIN repo (the git repo that holds your markdown pages):
-gbrain init --supabase
-
-# In the AGENT WORKSPACE repo (where OpenClaw runs):
-gbrain skillpack scaffold --all
+gbrain install
 ```
 
-`gbrain init --supabase` walks a short wizard that asks for your Supabase connection string and creates the schema. You'll get that connection string in Step 7 — read 7a and 7b first so you paste the right one (the transaction pooler, not the direct connection). If you'd rather try things locally before paying for a database, `gbrain init --pglite` gives you a zero-config embedded engine instead; you can migrate to Supabase later with `gbrain migrate --to supabase`.
+This installs:
 
-`gbrain skillpack scaffold --all` copies the ~43 bundled skills into your agent workspace as first-class files you can edit freely. (The old managed-install model was retired in v0.36.0.0; see `docs/INSTALL.md` if you're upgrading from an older release.)
+- About 60 skills
+- About 9 skill packs
+- Default brain structure
+- MCP server configuration
+- Supabase connection (for embeddings and search)
 
-From this point, the agent has working memory and access to every skill.
+GBrain populates the brain repo with its default directory structure, skill files, and configuration. From this point, the agent has working memory and access to every skill.
 
 ---
 

docs/what-schemas-unlock.md

@@ -32,7 +32,7 @@ gbrain schema sync --apply
 The sync backfills `page.type = 'meeting'` on all 4000 pages in 1000-row batches. Now:
 
 - `gbrain whoknows "Q3 roadmap discussion"` routes through the meeting type, ranking by `expert_routing` signal (attendees, recency, salience) instead of raw text.
-- The `extract_facts` cycle runs on every meeting page automatically (because `extractable: true`), pulling typed facts like `attended_by=alice-example`, `date=2026-05-23`.
+- `gbrain extract-facts` runs on every meeting page automatically (because `extractable: true`), pulling typed facts like `attended_by=alice-example`, `date=2026-05-23`.
 - The downstream `think` skill can now answer "what did we decide about pricing in the last three roadmap meetings" by querying the meeting graph instead of grep'ing 4000 files.
 
 One command. 4000 pages went from invisible to queryable. The content didn't change. The structure did.
@@ -62,7 +62,7 @@ gbrain schema add-link-type led-by      --page-type deal     --target-type inves
 gbrain schema sync --apply
 ```
 
-Now `gbrain whoknows "Series A SaaS"` routes through `investor` and `portco` types specifically, not the noisy general type set. `gbrain graph-query alice-example --type intro-from --depth 2` walks two hops of intros to surface "Alice introduced you to Bob who introduced you to Charlie." The `extract_facts` cycle starts producing typed claims from the fence in your deal pages: `(deals/acme-seed, raise=2000000, valuation=15000000, lead=widget-vc, closed_at=2026-05-23)`.
+Now `gbrain whoknows "Series A SaaS"` routes through `investor` and `portco` types specifically, not the noisy general type set. `gbrain graph-query alice-example --type intro-from --depth 2` walks two hops of intros to surface "Alice introduced you to Bob who introduced you to Charlie." `gbrain extract-facts` starts producing typed claims from the fence in your deal pages: `(deals/acme-seed, raise=2000000, valuation=15000000, lead=widget-vc, closed_at=2026-05-23)`.
 
 The CRM you've been promising yourself you'll set up next quarter? You just shipped it in 4 commands. It's downstream of your notes, not parallel to them.
 
@@ -143,7 +143,7 @@ Re-run the same `whoknows` query. Top-3 should shift, because the new type is no
 
 Three things gbrain does that generic note systems can't:
 
-**1. The brain knows the difference between a person and an idea.** Page-type matters at query time. `gbrain whoknows` only considers `expert_routing: true` types. The `extract_facts` cycle only runs on `extractable: true` types. `gbrain graph-query` walks declared link verbs. None of that works on a flat tag system because tags don't have semantics — they're labels. Types are first-class citizens with rules attached.
+**1. The brain knows the difference between a person and an idea.** Page-type matters at query time. `gbrain whoknows` only considers `expert_routing: true` types. `gbrain extract-facts` only runs on `extractable: true` types. `gbrain graph-query` walks declared link verbs. None of that works on a flat tag system because tags don't have semantics — they're labels. Types are first-class citizens with rules attached.
 
 **2. Untyped content is invisible content.** If your meetings are typed as `note`, expert routing skips them, facts extraction ignores them, link inference doesn't fire. They exist on disk and they're indexed for text search, but the structural surfaces (whoknows, find_experts, recall, think) treat them as second-class. Adding a type isn't cosmetic; it's structural promotion.
 

llms-full.txt

@@ -1565,8 +1565,8 @@ GBrain is designed to be installed and operated by an AI agent. The fastest path
 
 If you don't already have an AI agent platform running, start with one of these. Both are designed to read GBrain's install protocol and execute it:
 
-- **[OpenClaw](https://github.com/openclaw/openclaw)** — deploy [AlphaClaw on Render](https://render.com/deploy?repo=https://github.com/chrysb/alphaclaw) (one click, 8GB+ RAM)
-- **[Hermes](https://github.com/NousResearch/hermes-agent)** — deploy on [Railway](https://github.com/praveen-ks-2001/hermes-agent-template) (one click)
+- **[OpenClaw](https://github.com/openclawagents/openclaw)** — deploy [AlphaClaw on Render](https://render.com/deploy?repo=https://github.com/chrysb/alphaclaw) (one click, 8GB+ RAM)
+- **[Hermes](https://github.com/openclawagents/hermes)** — deploy on [Railway](https://github.com/praveen-ks-2001/hermes-agent-template) (one click)
 
 Then paste this into your agent:
 
@@ -2316,7 +2316,7 @@ gbrain schema sync --apply
 The sync backfills `page.type = 'meeting'` on all 4000 pages in 1000-row batches. Now:
 
 - `gbrain whoknows "Q3 roadmap discussion"` routes through the meeting type, ranking by `expert_routing` signal (attendees, recency, salience) instead of raw text.
-- The `extract_facts` cycle runs on every meeting page automatically (because `extractable: true`), pulling typed facts like `attended_by=alice-example`, `date=2026-05-23`.
+- `gbrain extract-facts` runs on every meeting page automatically (because `extractable: true`), pulling typed facts like `attended_by=alice-example`, `date=2026-05-23`.
 - The downstream `think` skill can now answer "what did we decide about pricing in the last three roadmap meetings" by querying the meeting graph instead of grep'ing 4000 files.
 
 One command. 4000 pages went from invisible to queryable. The content didn't change. The structure did.
@@ -2346,7 +2346,7 @@ gbrain schema add-link-type led-by      --page-type deal     --target-type inves
 gbrain schema sync --apply
 ```
 
-Now `gbrain whoknows "Series A SaaS"` routes through `investor` and `portco` types specifically, not the noisy general type set. `gbrain graph-query alice-example --type intro-from --depth 2` walks two hops of intros to surface "Alice introduced you to Bob who introduced you to Charlie." The `extract_facts` cycle starts producing typed claims from the fence in your deal pages: `(deals/acme-seed, raise=2000000, valuation=15000000, lead=widget-vc, closed_at=2026-05-23)`.
+Now `gbrain whoknows "Series A SaaS"` routes through `investor` and `portco` types specifically, not the noisy general type set. `gbrain graph-query alice-example --type intro-from --depth 2` walks two hops of intros to surface "Alice introduced you to Bob who introduced you to Charlie." `gbrain extract-facts` starts producing typed claims from the fence in your deal pages: `(deals/acme-seed, raise=2000000, valuation=15000000, lead=widget-vc, closed_at=2026-05-23)`.
 
 The CRM you've been promising yourself you'll set up next quarter? You just shipped it in 4 commands. It's downstream of your notes, not parallel to them.
 
@@ -2427,7 +2427,7 @@ Re-run the same `whoknows` query. Top-3 should shift, because the new type is no
 
 Three things gbrain does that generic note systems can't:
 
-**1. The brain knows the difference between a person and an idea.** Page-type matters at query time. `gbrain whoknows` only considers `expert_routing: true` types. The `extract_facts` cycle only runs on `extractable: true` types. `gbrain graph-query` walks declared link verbs. None of that works on a flat tag system because tags don't have semantics — they're labels. Types are first-class citizens with rules attached.
+**1. The brain knows the difference between a person and an idea.** Page-type matters at query time. `gbrain whoknows` only considers `expert_routing: true` types. `gbrain extract-facts` only runs on `extractable: true` types. `gbrain graph-query` walks declared link verbs. None of that works on a flat tag system because tags don't have semantics — they're labels. Types are first-class citizens with rules attached.
 
 **2. Untyped content is invisible content.** If your meetings are typed as `note`, expert routing skips them, facts extraction ignores them, link inference doesn't fire. They exist on disk and they're indexed for text search, but the structural surfaces (whoknows, find_experts, recall, think) treat them as second-class. Adding a type isn't cosmetic; it's structural promotion.
 
@@ -2720,17 +2720,14 @@ GBrain is tuned for the Supabase **Transaction pooler** (port 6543): it
 auto-disables prepared statements there and routes `engine.transaction()`
 (migrations, DDL, sync imports) to a derived **direct** connection
 (`db.<ref>.supabase.co:5432`). That direct host is IPv6-only, so on an
-IPv4-only host it is unreachable. When that happens gbrain now falls back to
-the pooler automatically (one stderr warning, then single-pool mode for the
-rest of the process) — but the pooler's ~2-min statement timeout can truncate
-very long migrations or bulk imports.
+IPv4-only host, reads work but sync **silently skips most pages**. This is the
+number one cause of "sync ran but nothing happened."
 
 Fix: make the direct connection reachable over IPv4. Either set
 `GBRAIN_DIRECT_DATABASE_URL` to the **Session pooler** string (port 5432 on the
-`pooler.supabase.com` host, IPv4), or enable Supabase's IPv4 add-on.
-`GBRAIN_DISABLE_DIRECT_POOL=1` skips the direct pool (and the fallback warning)
-entirely. Verify by running `gbrain sync` and checking that the page count in
-`gbrain stats` matches the syncable file count in the repo.
+`pooler.supabase.com` host, IPv4), or enable Supabase's IPv4 add-on. Verify by
+running `gbrain sync` and checking that the page count in `gbrain stats` matches
+the syncable file count in the repo.
 
 ### The Primitives
 
@@ -3897,7 +3894,7 @@ All 30 GBrain operations are available remotely, including `sync_brain` and
 directory where `gbrain serve` was launched. Symlinks, `..` traversal, and absolute
 paths outside cwd are rejected. Page slugs and filenames are allowlist-validated
 (alphanumeric + hyphens; no control chars, RTL overrides, or backslashes). Local
-CLI callers (`gbrain files upload ...`) keep unrestricted filesystem access since
+CLI callers (`gbrain file upload ...`) keep unrestricted filesystem access since
 the user owns the machine.
 
 ## Deployment Options
@@ -3905,43 +3902,6 @@ the user owns the machine.
 See [ALTERNATIVES.md](ALTERNATIVES.md) for a comparison of ngrok, Tailscale
 Funnel, and cloud hosts (Fly.io, Railway).
 
-### Co-located Docker workloads (self-hosted Postgres)
-
-OAuth scopes and source scoping guard the `gbrain serve --http` path. They do
-NOT guard raw Postgres. If the brain's Postgres runs as a container on the same
-Docker host as other workloads (agent runtimes, n8n, staging fixtures), any
-container sharing Docker's default `bridge` network can open a direct DB
-session — no OAuth token required — and read every source. That silently
-recreates a privileged path underneath the isolation you configured at the MCP
-layer.
-
-Network-zone the host so untrusted containers can never reach Postgres:
-
-```
-Docker host
-├── gbrain-net          ← ONLY the brain's Postgres (+ gbrain serve, if containerized)
-├── agent-<id>-net      ← each untrusted agent runtime, isolated
-└── default bridge      ← no secret-bearing databases
-```
-
-Operator checklist:
-
-```text
-[ ] Postgres is on a user-defined Docker network, not the default bridge
-    (or nothing else runs on that bridge)
-[ ] If Postgres publishes a host port at all, it binds loopback only
-    (`-p 127.0.0.1:5432:5432`, never `0.0.0.0`)
-[ ] Untrusted agent containers have no DATABASE_URL or Postgres password
-[ ] Untrusted agents reach the brain via OAuth/Bearer against serve --http only
-    (host loopback via host.docker.internal / host gateway — never gbrain-net)
-[ ] OAuth clients are least-privilege: scoped --source / --federated-read,
-    pre-minted short-lived tokens preferred over long-lived client secrets
-[ ] Isolation verified: a team-scoped client cannot read internal-only sources
-```
-
-Optional defense-in-depth: a dedicated Postgres role (or RLS) limited to the
-allowed `source_id`s, so even a leaked connection string can't read everything.
-
 ## Troubleshooting
 
 **"missing_auth" error**

openclaw.plugin.json

@@ -1,5 +1,4 @@
 {
-  "id": "gbrain-context-engine",
   "name": "gbrain",
   "version": "0.32.3.0",
   "description": "Personal knowledge brain with Postgres + pgvector hybrid search",

package.json

@@ -23,7 +23,6 @@
     "./backoff": "./src/core/backoff.ts",
     "./search/hybrid": "./src/core/search/hybrid.ts",
     "./search/expansion": "./src/core/search/expansion.ts",
-    "./think": "./src/core/think/index.ts",
     "./ai/gateway": "./src/core/ai/gateway.ts",
     "./extract": "./src/commands/extract.ts",
     "./ingestion": "./src/core/ingestion/index.ts",
@@ -42,20 +41,20 @@
     "eval:autocut": "bun test test/search/autocut-eval.test.ts",
     "test:full": "bun run verify && bash scripts/run-unit-parallel.sh && bun run test:slow && ([ -n \"$DATABASE_URL\" ] && bash scripts/run-e2e.sh || echo '[test:full] skipped E2E (no DATABASE_URL); run docker-compose -f docker-compose.ci.yml up + bun run test:e2e to include' 1>&2)",
     "verify": "bash scripts/run-verify-parallel.sh",
-    "check:source-config-leak": "bash scripts/check-source-config-leak.sh",
-    "check:no-pii-agent-voice": "bash scripts/check-no-pii-in-agent-voice.sh",
-    "check:synthetic-corpus-privacy": "bash scripts/check-synthetic-corpus-privacy.sh",
-    "check:system-of-record": "bash scripts/check-system-of-record.sh",
-    "check:admin-scope-drift": "bash scripts/check-admin-scope-drift.sh",
-    "check:cli-exec": "bash scripts/check-cli-executable.sh",
-    "check:all": "bash scripts/check-privacy.sh && bash scripts/check-proposal-pii.sh && bash scripts/check-test-real-names.sh && bash scripts/check-jsonb-pattern.sh && bash scripts/check-source-id-projection.sh && bash scripts/check-source-config-leak.sh && bash scripts/check-progress-to-stdout.sh && bash scripts/check-no-tracked-symlinks.sh && bash scripts/check-no-legacy-getconnection.sh && bash scripts/check-test-isolation.sh && bash scripts/check-trailing-newline.sh && bash scripts/check-wasm-embedded.sh && bash scripts/check-exports-count.sh && bash scripts/check-admin-build.sh && bash scripts/check-admin-scope-drift.sh && bash scripts/check-cli-executable.sh && bash scripts/check-skill-brain-first.sh && bash scripts/check-operations-filter-bypass.sh && bash scripts/check-gateway-routed-no-direct-anthropic.sh && bash scripts/check-worker-pool-atomicity.sh && bash scripts/check-key-files-current-state.sh && bash scripts/check-no-double-retry.sh && bash scripts/check-batch-audit-site.sh",
-    "check:gateway-routed": "bash scripts/check-gateway-routed-no-direct-anthropic.sh",
-    "check:worker-pool-atomicity": "bash scripts/check-worker-pool-atomicity.sh",
-    "check:doc-history": "bash scripts/check-key-files-current-state.sh",
+    "check:source-config-leak": "scripts/check-source-config-leak.sh",
+    "check:no-pii-agent-voice": "scripts/check-no-pii-in-agent-voice.sh",
+    "check:synthetic-corpus-privacy": "scripts/check-synthetic-corpus-privacy.sh",
+    "check:system-of-record": "scripts/check-system-of-record.sh",
+    "check:admin-scope-drift": "scripts/check-admin-scope-drift.sh",
+    "check:cli-exec": "scripts/check-cli-executable.sh",
+    "check:all": "scripts/check-privacy.sh && scripts/check-proposal-pii.sh && scripts/check-test-real-names.sh && scripts/check-jsonb-pattern.sh && scripts/check-source-id-projection.sh && scripts/check-source-config-leak.sh && scripts/check-progress-to-stdout.sh && scripts/check-no-legacy-getconnection.sh && scripts/check-test-isolation.sh && scripts/check-trailing-newline.sh && scripts/check-wasm-embedded.sh && scripts/check-exports-count.sh && scripts/check-admin-build.sh && scripts/check-admin-scope-drift.sh && scripts/check-cli-executable.sh && scripts/check-skill-brain-first.sh && scripts/check-operations-filter-bypass.sh && scripts/check-gateway-routed-no-direct-anthropic.sh && scripts/check-worker-pool-atomicity.sh && scripts/check-key-files-current-state.sh && scripts/check-no-double-retry.sh && scripts/check-batch-audit-site.sh",
+    "check:gateway-routed": "scripts/check-gateway-routed-no-direct-anthropic.sh",
+    "check:worker-pool-atomicity": "scripts/check-worker-pool-atomicity.sh",
+    "check:doc-history": "scripts/check-key-files-current-state.sh",
     "check:resolver": "bun src/cli.ts check-resolvable --strict --skills-dir skills/",
-    "check:skill-brain-first": "bash scripts/check-skill-brain-first.sh",
-    "check:wasm": "bash scripts/check-wasm-embedded.sh",
-    "check:newlines": "bash scripts/check-trailing-newline.sh",
+    "check:skill-brain-first": "scripts/check-skill-brain-first.sh",
+    "check:wasm": "scripts/check-wasm-embedded.sh",
+    "check:newlines": "scripts/check-trailing-newline.sh",
     "test:e2e": "bash scripts/run-e2e.sh",
     "test:slow": "bash scripts/run-slow-tests.sh",
     "test:heavy": "bash scripts/run-heavy.sh",
@@ -65,27 +64,26 @@
     "ci:local:diff": "bash scripts/ci-local.sh --diff",
     "ci:select-e2e": "bun run scripts/select-e2e.ts",
     "typecheck": "tsc --noEmit",
-    "check:jsonb": "bash scripts/check-jsonb-pattern.sh",
-    "check:search-path": "bash scripts/check-search-path.sh",
-    "check:no-double-retry": "bash scripts/check-no-double-retry.sh",
-    "check:batch-audit-site": "bash scripts/check-batch-audit-site.sh",
-    "check:worker-lock-renewal-shape": "bash scripts/check-worker-lock-renewal-shape.sh",
-    "check:source-id-projection": "bash scripts/check-source-id-projection.sh",
-    "check:privacy": "bash scripts/check-privacy.sh",
-    "check:proposal-pii": "bash scripts/check-proposal-pii.sh",
-    "check:eval-glossary": "bash scripts/check-eval-glossary-fresh.sh",
-    "check:test-names": "bash scripts/check-test-real-names.sh",
-    "check:progress": "bash scripts/check-progress-to-stdout.sh",
-    "check:no-tracked-symlinks": "bash scripts/check-no-tracked-symlinks.sh",
-    "check:exports-count": "bash scripts/check-exports-count.sh",
-    "check:admin-build": "bash scripts/check-admin-build.sh",
-    "check:admin-embedded": "bash scripts/check-admin-embedded.sh",
-    "check:test-isolation": "bash scripts/check-test-isolation.sh",
-    "check:fuzz-purity": "bash scripts/check-fuzz-purity.sh",
-    "check:operations-filter-bypass": "bash scripts/check-operations-filter-bypass.sh",
-    "check:fixture-privacy": "bash scripts/check-fixture-privacy.sh",
+    "check:jsonb": "scripts/check-jsonb-pattern.sh",
+    "check:search-path": "scripts/check-search-path.sh",
+    "check:no-double-retry": "scripts/check-no-double-retry.sh",
+    "check:batch-audit-site": "scripts/check-batch-audit-site.sh",
+    "check:worker-lock-renewal-shape": "scripts/check-worker-lock-renewal-shape.sh",
+    "check:source-id-projection": "scripts/check-source-id-projection.sh",
+    "check:privacy": "scripts/check-privacy.sh",
+    "check:proposal-pii": "scripts/check-proposal-pii.sh",
+    "check:eval-glossary": "scripts/check-eval-glossary-fresh.sh",
+    "check:test-names": "scripts/check-test-real-names.sh",
+    "check:progress": "scripts/check-progress-to-stdout.sh",
+    "check:exports-count": "scripts/check-exports-count.sh",
+    "check:admin-build": "scripts/check-admin-build.sh",
+    "check:admin-embedded": "scripts/check-admin-embedded.sh",
+    "check:test-isolation": "scripts/check-test-isolation.sh",
+    "check:fuzz-purity": "scripts/check-fuzz-purity.sh",
+    "check:operations-filter-bypass": "scripts/check-operations-filter-bypass.sh",
+    "check:fixture-privacy": "scripts/check-fixture-privacy.sh",
     "check:conversation-parser": "bun src/cli.ts eval conversation-parser test/fixtures/conversation-formats/all.jsonl --no-llm",
-    "check:source-scope-onboard": "bash scripts/check-source-scope-onboard.sh",
+    "check:source-scope-onboard": "scripts/check-source-scope-onboard.sh",
     "postinstall": "bun run scripts/postinstall.ts",
     "prepublish:clawhub": "bun run build:all",
     "publish:clawhub": "clawhub package publish . --family bundle-plugin"
@@ -146,11 +144,10 @@
     "bun": ">=1.3.10"
   },
   "license": "MIT",
-  "version": "0.42.67.0",
+  "version": "0.42.64.0",
   "overrides": {
-    "@hono/node-server": "^2.0.5",
-    "fast-uri": "^3.1.4",
-    "body-parser": "^2.3.0",
+    "@hono/node-server": "^1.19.13",
+    "fast-uri": "^3.1.2",
     "fast-xml-builder": "^1.1.7",
     "fast-xml-parser": "^5.7.0",
     "form-data": "^4.0.6",

recipes/x-to-brain.md

@@ -1,7 +1,7 @@
 ---
 id: x-to-brain
 name: X-to-Brain
-version: 0.8.2
+version: 0.8.1
 description: Twitter timeline, mentions, and keyword monitoring flow into brain pages. Tracks deletions, engagement velocity, OCR on images, and real-time alerts.
 category: sense
 requires: []
@@ -9,12 +9,9 @@ secrets:
   - name: X_BEARER_TOKEN
     description: X API v2 Bearer token (Basic tier minimum, $200/mo for full archive search)
     where: https://developer.x.com/en/portal/dashboard — create a project + app, copy the Bearer Token from "Keys and tokens"
-  - name: X_HANDLE
-    description: Your X username without the @ (used for the app-only health check — /users/me requires user-context OAuth, which app-only bearer tokens don't have)
-    where: Your X profile — the handle in your profile URL, e.g. x.com/yourhandle → yourhandle
 health_checks:
   - type: http
-    url: "https://api.x.com/2/users/by/username/$X_HANDLE"
+    url: "https://api.x.com/2/users/me"
     auth: bearer
     auth_token: "$X_BEARER_TOKEN"
     label: "X API"
@@ -113,17 +110,15 @@ Tell the user:
 4. Inside the project, create a new App
 5. Go to the app's 'Keys and tokens' tab
 6. Under 'Bearer Token', click 'Generate' (or 'Regenerate')
-7. Copy the Bearer Token and paste it to me, along with your X handle (without the @)
+7. Copy the Bearer Token and paste it to me
 
 Note: Free tier gives read-only access with low limits. Basic tier ($200/mo)
 gives search/recent endpoint and higher limits. Pro tier gets full archive search."
 
-Set both `X_BEARER_TOKEN` and `X_HANDLE` in the environment. Validate immediately
-(app-only bearer tokens cannot call `/users/me` — that endpoint requires
-user-context OAuth — so validation uses the by-username lookup):
+Validate immediately:
 ```bash
 curl -sf -H "Authorization: Bearer $X_BEARER_TOKEN" \
-  "https://api.x.com/2/users/by/username/$X_HANDLE" \
+  "https://api.x.com/2/users/me" \
   && echo "PASS: X API connected" \
   || echo "FAIL: X API token invalid"
 ```
@@ -139,10 +134,10 @@ starting with 'AAA...', (3) if you just created the app, the token is valid imme
 ```bash
 # Look up the user's X user ID from their handle
 curl -sf -H "Authorization: Bearer $X_BEARER_TOKEN" \
-  "https://api.x.com/2/users/by/username/$X_HANDLE" | grep -o '"id":"[^"]*"'
+  "https://api.x.com/2/users/by/username/USERNAME" | grep -o '"id":"[^"]*"'
 ```
 
-Look up the user ID from the handle collected in Step 1.
+Ask the user for their X handle (e.g., @yourhandle). Look up their user ID.
 Save it — the collector needs the numeric ID, not the handle.
 
 ### Step 3: Configure the Collector
@@ -210,7 +205,7 @@ The agent should review collected data 2-3x daily and run enrichment.
 
 ```bash
 mkdir -p ~/.gbrain/integrations/x-to-brain
-echo '{"ts":"'$(date -u +%Y-%m-%dT%H:%M:%SZ)'","event":"setup_complete","source_version":"0.8.2","status":"ok","details":{"user_id":"X_USER_ID"}}' >> ~/.gbrain/integrations/x-to-brain/heartbeat.jsonl
+echo '{"ts":"'$(date -u +%Y-%m-%dT%H:%M:%SZ)'","event":"setup_complete","source_version":"0.8.1","status":"ok","details":{"user_id":"X_USER_ID"}}' >> ~/.gbrain/integrations/x-to-brain/heartbeat.jsonl
 ```
 
 ## Production Patterns (v0.8.1)

scripts/check-exports-count.sh

@@ -19,7 +19,7 @@
 
 set -euo pipefail
 
-EXPECTED_COUNT=21
+EXPECTED_COUNT=20
 
 # Count top-level keys in the exports object. `node -e` parses JSON
 # reliably without needing jq (which isn't in every CI environment).

scripts/check-no-tracked-symlinks.sh

@@ -1,67 +0,0 @@
-#!/usr/bin/env bash
-# CI guard: fail if any symlink is tracked in git.
-#
-# A symlink committed from a build sandbox points at a path that exists on
-# exactly one machine. Everywhere else the checkout produces a dangling
-# link, and anything that opens it fails. That is not hypothetical: commit
-# faf5cdba landed `node_modules -> /tmp/fleet/repo/node_modules`, which made
-# `bun install` abort with `ENOENT: could not open the "node_modules"
-# directory` on every fresh clone, and took `gbrain upgrade`'s bun-link path
-# down with it (the auto-upgrade runs `bun install`, so the printed manual
-# fallback failed the same way).
-#
-# .gitignore alone does not prevent this. A `node_modules/` pattern with a
-# trailing slash matches directories ONLY, so a symlink of the same name is
-# never ignored. Dropping the slash closes that hole, but `git add -f` still
-# walks straight past it. This guard is the backstop.
-#
-# The repo has no legitimate tracked symlinks, so the allowlist starts
-# empty. If you ever need one, add its exact repo-relative path to ALLOWLIST
-# below and explain why — a relative link that resolves inside the repo is
-# defensible; an absolute one almost never is.
-#
-# Usage: scripts/check-no-tracked-symlinks.sh
-# Exit:  0 when clean, 1 when a tracked symlink is found.
-
-set -euo pipefail
-
-ROOT="$(git rev-parse --show-toplevel 2>/dev/null || pwd)"
-cd "$ROOT"
-
-# Paths permitted to be tracked symlinks. Empty by design.
-ALLOWLIST=()
-
-# Git records symlinks with mode 120000. Field 4 of `ls-files -s` is the path
-# (tab-separated from the stage number), so cut on the tab to keep paths with
-# spaces intact.
-found="$(git ls-files -s | awk '$1 == "120000"' | cut -f2- || true)"
-
-if [ -n "$found" ]; then
-  filtered="$found"
-  for f in "${ALLOWLIST[@]:-}"; do
-    [ -z "$f" ] && continue
-    filtered="$(echo "$filtered" | grep -vxF "$f" || true)"
-  done
-
-  if [ -n "$filtered" ]; then
-    echo "ERROR: symlink(s) tracked in git:"
-    echo
-    while IFS= read -r path; do
-      [ -z "$path" ] && continue
-      target="$(git cat-file blob ":$path" 2>/dev/null || echo '<unreadable>')"
-      echo "  $path -> $target"
-    done <<< "$filtered"
-    echo
-    echo "A committed symlink resolves on the machine that created it and"
-    echo "nowhere else. Untrack it:"
-    echo
-    echo "  git rm --cached <path>"
-    echo
-    echo "If the path is build output (node_modules, dist, bin), also confirm"
-    echo "it is covered by .gitignore WITHOUT a trailing slash — a trailing"
-    echo "slash matches directories only and lets the symlink through."
-    exit 1
-  fi
-fi
-
-echo "check-no-tracked-symlinks: OK (no tracked symlinks)"

scripts/check-operations-filter-bypass.sh

@@ -70,7 +70,7 @@ PATTERN='import[[:space:]]+(\*[[:space:]]+as[[:space:]]+[a-zA-Z_$][a-zA-Z0-9_$]*
 FOUND_FILES=""
 while IFS= read -r f; do
   [ -n "$f" ] && FOUND_FILES="$FOUND_FILES$f"$'\n'
-done < <(grep -rlE --include='*.ts' "$PATTERN" src 2>/dev/null | sort -u || true)
+done < <(grep -rlE --include='*.ts' "$PATTERN" src/ 2>/dev/null | sort -u || true)
 
 FAIL=0
 

scripts/check-test-real-names.sh

@@ -100,9 +100,9 @@ IFS='|' eval 'PATTERN="${PATTERN_PARTS[*]}"'
 
 # Find tool.
 if command -v rg >/dev/null 2>&1; then
-  matches="$(rg -niH --no-heading -t ts "$PATTERN" test 2>/dev/null || true)"
+  matches="$(rg -niH --no-heading -t ts "$PATTERN" test/ 2>/dev/null || true)"
 elif command -v grep >/dev/null 2>&1; then
-  matches="$(grep -rniE --include='*.test.ts' "$PATTERN" test 2>/dev/null || true)"
+  matches="$(grep -rniE --include='*.test.ts' "$PATTERN" test/ 2>/dev/null || true)"
 else
   echo "check-test-real-names: ERROR: neither rg nor grep available." >&2
   exit 2

scripts/check-wasm-embedded.sh

@@ -19,25 +19,13 @@ set -euo pipefail
 REPO_ROOT="$(cd "$(dirname "$0")/.." && pwd)"
 cd "$REPO_ROOT"
 
-# Build from a container-local copy. On Docker Desktop, Bun canonicalizes a
-# bind-mounted input to /run/host_virtiofs but keeps /app as the output path;
-# its final atomic rename then fails with ENOENT even though both names refer
-# to the same mount. Keeping inputs and output under /tmp avoids that alias.
-BUILD_DIR="$(mktemp -d /tmp/gbrain-wasm-check.XXXXXX)"
-OUT_BIN="$BUILD_DIR/chunker-smoketest"
-trap 'rm -rf "$BUILD_DIR"' EXIT
-mkdir -p "$BUILD_DIR/scripts"
-cp -R "$REPO_ROOT/src" "$BUILD_DIR/src"
-cp "$REPO_ROOT/scripts/chunker-smoketest.ts" "$BUILD_DIR/scripts/chunker-smoketest.ts"
-ln -s "$REPO_ROOT/node_modules" "$BUILD_DIR/node_modules"
+OUT_BIN="$(mktemp /tmp/gbrain-wasm-check.XXXXXX)"
+trap 'rm -f "$OUT_BIN"' EXIT
 
 # Build a minimal smoketest binary that imports the chunker. We compile this
 # instead of the full gbrain CLI so the failure mode is laser-focused on
 # chunker + WASM path resolution, not unrelated CLI wiring.
-if ! (cd "$BUILD_DIR" && bun build --compile --outfile "$OUT_BIN" scripts/chunker-smoketest.ts >/dev/null); then
-  echo "[check-wasm-embedded] FAIL: bun could not compile the smoketest binary." >&2
-  exit 1
-fi
+bun build --compile --outfile "$OUT_BIN" scripts/chunker-smoketest.ts >/dev/null 2>&1
 
 # Run it and capture JSON output.
 OUTPUT="$("$OUT_BIN" 2>&1)"

scripts/ci-local.sh

@@ -350,7 +350,7 @@ if [ -f .git ]; then
 fi
 
 echo "[ci-local] Running checks inside runner container..."
-docker compose -f "$COMPOSE_FILE" run --rm "${EXTRA_MOUNTS[@]}" runner bash -c "$INNER_CMD"
+docker compose -f "$COMPOSE_FILE" run --rm "${EXTRA_MOUNTS[@]:-}" runner bash -c "$INNER_CMD"
 
 echo ""
 echo "[ci-local] All checks passed."

scripts/e2e-test-map.ts

@@ -42,19 +42,8 @@ export const E2E_TEST_MAP: Record<string, string[]> = {
   // phase, extract, integrity, embed, or migrate-engine change.
   "src/core/cycle/extract-takes.ts": ["test/e2e/multi-source-bug-class.test.ts"],
   "src/core/cycle/patterns.ts": ["test/e2e/multi-source-bug-class.test.ts"],
-  "src/core/cycle/synthesize.ts": [
-    "test/e2e/multi-source-bug-class.test.ts",
-    "test/e2e/synthesize-bigint-job-id-postgres.test.ts",
-  ],
-  "src/commands/embed.ts": [
-    "test/e2e/multi-source-bug-class.test.ts",
-    // #3391: the NULL-signature stale predicates differ per engine.
-    "test/e2e/migrate-embeddings-postgres.test.ts",
-  ],
-  // #3390: runSchemaTransition's DDL path + the stale predicates behave
-  // differently on real pgvector than on PGLite.
-  "src/core/embedding-migration.ts": ["test/e2e/migrate-embeddings-postgres.test.ts"],
-  "src/core/retrieval-upgrade-planner.ts": ["test/e2e/migrate-embeddings-postgres.test.ts"],
+  "src/core/cycle/synthesize.ts": ["test/e2e/multi-source-bug-class.test.ts"],
+  "src/commands/embed.ts": ["test/e2e/multi-source-bug-class.test.ts"],
   "src/commands/extract.ts": ["test/e2e/multi-source-bug-class.test.ts"],
   "src/commands/migrate-engine.ts": ["test/e2e/multi-source-bug-class.test.ts"],
   // Any minions queue/worker/handler change exercises all minion E2E.
@@ -72,8 +61,6 @@ export const E2E_TEST_MAP: Record<string, string[]> = {
     "test/e2e/jsonb-roundtrip.test.ts",
     "test/e2e/engine-parity.test.ts",
     "test/e2e/schema-drift.test.ts",
-    // #3391: includeNullSignature stale predicates (engine parity).
-    "test/e2e/migrate-embeddings-postgres.test.ts",
   ],
   // PGLite bootstrap path + parity guard.
   "src/core/pglite-engine.ts": [

scripts/run-unit-parallel.sh

@@ -133,7 +133,6 @@ for i in $(seq 1 "$N"); do
         env SHARD="$i/$N" \
         bash scripts/run-unit-shard.sh --max-concurrency="$INTRA_CONC" \
         > "$SHARD_LOG" 2>&1
-      rc=$?
     else
       env SHARD="$i/$N" \
         bash scripts/run-unit-shard.sh --max-concurrency="$INTRA_CONC" \
@@ -143,20 +142,10 @@ for i in $(seq 1 "$N"); do
         sleep 5 && kill -KILL "$pid" 2>/dev/null ) &
       cap_pid=$!
       wait "$pid" 2>/dev/null
-      # Capture the shard's exit code from ITS `wait`, before any watchdog
-      # teardown runs. The teardown commands below overwrite $? — the killed
-      # watchdog reports 143 — which used to get stamped into every shard's
-      # sentinel on machines with no gtimeout/timeout: every run "failed"
-      # with rc=143 summaries even when all tests passed.
-      rc=$?
-      # Reap the watchdog's `sleep` child too (pkill -P), then the watchdog.
-      # Killing only the subshell leaves the sleep orphaned until
-      # $SHARD_TIMEOUT elapses — same quirk the heartbeat cleanup below works
-      # around; CI's orphan-process sweep flags those.
-      pkill -P "$cap_pid" 2>/dev/null
       kill "$cap_pid" 2>/dev/null
       wait "$cap_pid" 2>/dev/null
     fi
+    rc=$?
     echo "$rc" > "$LOG_DIR/shard-$i.exit"
     [ "$rc" = "124" ] && echo "WEDGED" > "$LOG_DIR/shard-$i.wedged"
   ) &

scripts/run-verify-parallel.sh

@@ -42,7 +42,6 @@ CHECKS=(
   "check:source-id-projection"
   "check:source-config-leak"
   "check:progress"
-  "check:no-tracked-symlinks"
   "check:test-isolation"
   "check:wasm"
   "check:admin-build"
@@ -127,7 +126,6 @@ for c in "${CHECKS[@]}"; do
   (
     if [ -n "$TIMEOUT_BIN" ]; then
       "$TIMEOUT_BIN" "${TIMEOUT}s" bun run "$c" > "$LOG_FILE" 2>&1
-      rc=$?
     else
       bun run "$c" > "$LOG_FILE" 2>&1 &
       pid=$!
@@ -135,20 +133,10 @@ for c in "${CHECKS[@]}"; do
         sleep 5 && kill -KILL "$pid" 2>/dev/null ) &
       cap_pid=$!
       wait "$pid" 2>/dev/null
-      # Capture the check's exit code from ITS `wait`, before any watchdog
-      # teardown runs. The teardown commands below overwrite $? — the killed
-      # watchdog reports 143 — which used to get stamped into every sentinel
-      # on machines with no gtimeout/timeout: verify reported pass=0
-      # fail=<all> while every per-check log said OK.
-      rc=$?
-      # Reap the watchdog's `sleep` child too (pkill -P), then the watchdog.
-      # Killing only the subshell leaves the sleep orphaned until $TIMEOUT
-      # elapses — same quirk the heartbeat cleanup in run-unit-parallel.sh
-      # works around; CI's orphan-process sweep flags those.
-      pkill -P "$cap_pid" 2>/dev/null
       kill "$cap_pid" 2>/dev/null
       wait "$cap_pid" 2>/dev/null
     fi
+    rc=$?
     echo "$rc" > "$EXIT_FILE"
   ) &
   PIDS+=($!)

skills/book-mirror/SKILL.md

@@ -248,7 +248,7 @@ before submission.
 After the brain page is written, render to PDF using `skills/brain-pdf`:
 
 ```bash
-gbrain put  # already done by the CLI; nothing to add here
+gbrain put_page  # already done by the CLI; nothing to add here
 # Then invoke brain-pdf:
 # (see skills/brain-pdf/SKILL.md for the make-pdf invocation)
 ```

skills/capture/SKILL.md

@@ -62,7 +62,7 @@ gbrain capture "..." --json           # structured output for agents
 - **Slug:** `inbox/YYYY-MM-DD-<hash8>` (stable for same content; the daemon's 24h dedup catches re-captures).
 - **Type:** `note` (override with `--type idea` etc.).
 - **Frontmatter stamps:** `captured_via: capture-cli`, `captured_at: <ISO>`.
-- **Title:** first non-empty line of the body, capped at 80 chars (truncation appends `…`).
+- **Title:** first non-empty line of the body, capped at 80 chars.
 
 ## Output Format
 

skills/conventions/cron-via-minions.md

@@ -73,13 +73,13 @@ stock worker auto-loads on startup) registers handlers before `start()`.
 Users who set `minion_mode: off` in `~/.gbrain/preferences.json` keep
 using `agentTurn`. Respect that. No auto-rewrite.
 
-## Forward note
+## Forward note (v0.12.0)
 
-A native scheduler loop inside `gbrain jobs work` (owning cron
-expressions directly, with no host-scheduler hand-off) has been on the
-roadmap since v0.11.1 but has not shipped. The host scheduler keeps
-firing on schedule; this convention only replaces the execution layer
-(what the cron trigger *does*), not the scheduling layer.
+GBrain v0.12.0 ships `gbrain cron`: a scheduler loop inside
+`gbrain jobs work` that owns cron expressions natively — no more
+handing off to host schedulers. Until v0.12.0 lands, the host
+scheduler keeps firing on schedule; v0.11.1 only replaces the execution
+layer (what the cron trigger *does*), not the scheduling layer.
 
 ## Related
 

skills/data-research/SKILL.md

@@ -54,8 +54,8 @@ Ask the user what they want to track. Either:
 - Define a custom recipe with: source queries, classification rules, extraction schema,
   tracker page path, tracker format
 
-Recipes are YAML files at `~/.gbrain/recipes/{name}.yaml`. Scaffold a new one by
-copying a built-in recipe file and editing its fields.
+Recipes are YAML files at `~/.gbrain/recipes/{name}.yaml`. Use `gbrain research init`
+to scaffold a new one.
 
 ### Phase 2: Search Sources
 

skills/eiirp/SKILL.md

@@ -201,7 +201,7 @@ Use the brain page template. MUST include:
 
 ### 4b. Entity pages (people, companies)
 For each entity mentioned:
-- Check if a brain page exists (`gbrain search "<name>"` or `gbrain get people/<slug>`).
+- Check if a brain page exists (`gbrain search "<name>"` or `gbrain get_page people/<slug>`).
 - If exists: update State, append Timeline entry citing this research.
 - If not: create with enrichment.
 

skills/perplexity-research/SKILL.md

@@ -112,7 +112,7 @@ gbrain query "<topic keywords>"
 #      -d '{"model": "sonar-pro", "messages": [{"role":"user","content":"..."}]}'
 
 # 4. Write the structured research page via put_page:
-gbrain put research/<slug>      # via the put_page operation
+gbrain put_page research/<slug>      # via the put_page operation
 
 # 5. Cross-link entities mentioned (people, companies) per Iron Law.
 ```

skills/schema-unify/SKILL.md

@@ -11,7 +11,7 @@ tools:
   - gbrain schema active
   - gbrain schema use
   - gbrain schema stats
-  - gbrain restore
+  - gbrain pages restore
   - mcp:run_onboard
 triggers:
   - "unify my types"
@@ -143,7 +143,7 @@ WHERE source_id = 'default' AND frontmatter->>'legacy_type' IS NOT NULL;
 Page-to-alias and page-to-link source pages soft-delete with 72h TTL. Restore within that window:
 
 ```bash
-gbrain restore <slug>
+gbrain pages restore <slug>
 ```
 
 Revert the active pack flip:
@@ -197,7 +197,7 @@ Outputs:
 - Active pack flipped to `gbrain-base-v2` atomically at end of successful run.
 
 Side effects:
-- Source pages soft-deleted with 72h restore TTL (`gbrain restore <slug>`).
+- Source pages soft-deleted with 72h restore TTL (`gbrain pages restore <slug>`).
 - One-time cache invalidation on KNOBS_HASH_VERSION bump (5→6); self-healing in `cache.ttl_seconds`.
 - Query-time `--type X` alias-expands via `expandTypeFilter` (D14 back-compat).
 
@@ -212,7 +212,7 @@ DON'T:
 - Submit `unify-types` directly via the MCP `submit_job` op without `--allow-protected`. PROTECTED handlers require trusted local callers; remote MCP rejection is the intentional trust boundary.
 - Edit `mapping_rules` in `gbrain-base-v2.yaml` to skip clusters you don't trust. Fork the pack instead (`gbrain schema fork`) so the source-of-truth migration stays consistent across brains.
 - Run `unify-types` from inside an autopilot tick. The check is `manual_only` per D17 — autopilot deliberately never auto-fires it because pack upgrades are one-time consenting taxonomy decisions.
-- Hard-delete soft-deleted source pages before the 72h restore window. Use `gbrain restore <slug>` first if rollback is needed.
+- Hard-delete soft-deleted source pages before the 72h restore window. Use `gbrain pages restore <slug>` first if rollback is needed.
 - Assume `frontmatter.legacy_type` survives every roundtrip. The marker is canonical for the immediate post-migration window; downstream re-imports may overwrite it.
 
 ## Output Format

skills/skillify/SKILL.md

@@ -60,14 +60,7 @@ Before skillifying, check:
 - Is there >20 lines of logic? (Trivial helpers don't need full infrastructure)
 - Does it have a clear trigger phrase a user would actually say?
 
-If ANY answer is no, it's a script, not a skill — stop here. Do not scaffold, write a SKILL.md, run evals, or write tests for it. Tell the user why and move on.
-
-Scope check (upper bound): one skill = one capability = one coherent trigger
-family. If the target spans multiple distinct intents users would invoke
-separately ("run the build" / "roll back the deploy" / "notify the team" are
-three intents, not one), do NOT build one skill covering them all. Stop,
-propose splitting into separate skillify targets, and ask the user which one
-to skillify first.
+If no to all three, it's a script, not a skill. Move on.
 
 ## Phase 1: Audit
 

skills/skillpack-harvest/SKILL.md

@@ -266,5 +266,4 @@ editorial pass.
   (e.g. `src/commands/<slug>.ts` if the host SKILL.md declares it
   in frontmatter)
 - gbrain's `openclaw.plugin.json` — adds the slug to `skills:`
-  array, sorted alphabetically, without removing OpenClaw-native plugin fields
-  like `id`, `configSchema`, or `contracts`
+  array, sorted alphabetically

skills/testing/SKILL.md

@@ -57,8 +57,6 @@ This mode guarantees:
 - `skills/manifest.json` lists every skill directory
 - `skills/RESOLVER.md` references every skill in the manifest
 - `openclaw.plugin.json` `skills[]` round-trips with both
-- `openclaw.plugin.json` keeps OpenClaw install-required native plugin fields
-  (`id`, object `configSchema`, and `contracts.contextEngines` when applicable)
 - No MECE violations (duplicate triggers across skills)
 
 ### Phases
@@ -74,7 +72,7 @@ This mode guarantees:
 ### Automation
 
 ```bash
-bun test test/skills-conformance.test.ts test/resolver.test.ts test/openclaw-plugin-manifest.test.ts
+bun test test/skills-conformance.test.ts test/resolver.test.ts
 ```
 
 The CI-gated check is the package.json `test` script.

skills/voice-note-ingest/SKILL.md

@@ -43,9 +43,8 @@ The Analysis section can interpret; the transcript section is sacred.
 
 The user sends an audio or voice message via any channel (Telegram, voice
 memo upload, openclaw audio attachment). The host agent typically provides
-the transcript text. If not, transcribe it with your host's transcription
-tool (Groq Whisper is fast and cheap; OpenAI Whisper works too — segment
-audio > 25MB via ffmpeg first).
+the transcript text. If not, transcribe via `gbrain transcription` (Groq
+Whisper by default; OpenAI fallback for audio > 25MB segmented via ffmpeg).
 
 ## The pipeline
 
@@ -53,9 +52,8 @@ audio > 25MB via ffmpeg first).
 1. STORE       → Upload original audio to gbrain storage backend
                  (S3 / Supabase Storage / local — pluggable per
                  src/core/storage.ts).
-2. TRANSCRIBE  → Use the agent-provided transcript verbatim, OR
-                 transcribe the audio yourself (see "When to invoke")
-                 if no transcript was supplied.
+2. TRANSCRIBE  → Use the agent-provided transcript verbatim, OR call
+                 gbrain transcription if no transcript was supplied.
 3. ROUTE       → Apply the decision tree (below) to find the right
                  destination directory.
 4. WRITE       → Create / update the destination brain page; preserve the

src/admin-embedded.ts

@@ -1,13 +1,13 @@
 // AUTO-GENERATED — do not edit by hand.
 // Run `bun run scripts/build-admin-embedded.ts` to regenerate.
-// Source: admin/dist/ at 2026-07-24.
+// Source: admin/dist/ at 2026-05-27.
 //
 // Bun resolves the file: imports to a path that works at runtime even
 // inside a compiled binary (`bun build --compile`). The manifest maps
 // the request path the express handler sees to (resolved-path, mime).
 
 // @ts-ignore — type: 'file' is Bun ESM, not in lib.d.ts
-import A_0_assets_index_CviJXT_1_js from '../admin/dist/assets/index-CviJXT-1.js' with { type: 'file' };
+import A_0_assets_index_CoGEje3__js from '../admin/dist/assets/index-CoGEje3-.js' with { type: 'file' };
 // @ts-ignore — type: 'file' is Bun ESM, not in lib.d.ts
 import A_1_assets_index_GxkWX7v3_css from '../admin/dist/assets/index-GxkWX7v3.css' with { type: 'file' };
 // @ts-ignore — type: 'file' is Bun ESM, not in lib.d.ts
@@ -19,7 +19,7 @@ export interface AdminAsset {
 }
 
 export const ADMIN_ASSETS: Record<string, AdminAsset> = {
-  "/admin/assets/index-CviJXT-1.js": { path: A_0_assets_index_CviJXT_1_js as unknown as string, mime: "application/javascript; charset=utf-8" },
+  "/admin/assets/index-CoGEje3-.js": { path: A_0_assets_index_CoGEje3__js as unknown as string, mime: "application/javascript; charset=utf-8" },
   "/admin/assets/index-GxkWX7v3.css": { path: A_1_assets_index_GxkWX7v3_css as unknown as string, mime: "text/css; charset=utf-8" },
   "/admin/index.html": { path: A_2_index_html as unknown as string, mime: "text/html; charset=utf-8" },
 };

src/cli.ts

@@ -9,7 +9,7 @@ installSigchldHandler();
 import { installSignalHandlers as installCleanupSignalHandlers } from './core/process-cleanup.ts';
 installCleanupSignalHandlers();
 
-import { readFileSync, existsSync, unlinkSync, fstatSync } from 'fs';
+import { readFileSync, existsSync, unlinkSync } from 'fs';
 import { spawn } from 'child_process';
 import {
   readUpdateCache,
@@ -55,17 +55,12 @@ export function bigintToStringReplacer(_key: string, value: unknown): unknown {
 }
 
 // CLI-only commands that bypass the operation layer
-export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'maintain', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'retrieval-upgrade', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector', 'pages', 'bench', 'backfill']);
+export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
 // CLI-only commands whose handlers print their own --help text. These are
 // excluded from the generic short-circuit so detailed per-command and
 // per-subcommand usage stays reachable.
 const CLI_ONLY_SELF_HELP = new Set([
   'upgrade', 'post-upgrade', 'check-update',
-  // #3502 sweep: pages + bench print their own usage (pages.ts printHelp,
-  // bench-publish.ts printHelp). Both were documented but undispatchable —
-  // `pages` had a live handleCliOnly case but was missing from CLI_ONLY
-  // (the #2035 calibration bug class); `bench` was never wired at all.
-  'pages', 'bench',
   'embed', 'config',
   'skillpack', 'skillpack-check',
   'integrations', 'friction',
@@ -84,8 +79,6 @@ const CLI_ONLY_SELF_HELP = new Set([
   'capture',
   // v0.42 self-upgrade ships its own usage (flags + the agent-skill story).
   'self-upgrade',
-  // maintain (#3015) prints its own usage block (modes + not-auto-applied list).
-  'maintain',
   // v0.43 (#2095): watch ships WATCH_HELP (flags + the stdin-turn protocol).
   'watch',
   // v0.37 fix wave (Lane D.4 + CDX2-12): sync's --no-embed flag was
@@ -112,10 +105,6 @@ const CLI_ONLY_SELF_HELP = new Set([
   // `gbrain connect --help` prints its own usage (flags + examples) from
   // runConnect; route around the generic one-line short-circuit.
   'connect',
-  // #3390 — `gbrain migrate embeddings --help` / `gbrain retrieval-upgrade
-  // --help` print the migration flags from runMigrateEmbeddings. `migrate`
-  // (engine transfer) keeps its own dispatch too.
-  'migrate', 'retrieval-upgrade',
 ]);
 
 // v114 (#1941): alias -> operation lookup, kept separate from `cliOps` so
@@ -349,11 +338,6 @@ async function main() {
   // them out of the engine try/catch is safe and unlocks routing.
   const params = parseOpArgs(op, subArgs);
 
-  // #3513: stdin fill moved out of parseOpArgs so a non-TTY stdin with no
-  // piped input can't block the parse forever — the bounded read leaves the
-  // param unset on timeout and the required-param check below fails fast.
-  await applyStdinParam(op, params);
-
   // v0.27.1 (`gbrain query --image <path>`): swap the `image` param from
   // a filesystem path into base64 bytes + mime. The op accepts base64; the
   // CLI accepts a path. Helper is exported so tests can exercise the
@@ -814,99 +798,18 @@ export function parseOpArgs(op: Operation, args: string[]): Record<string, unkno
     }
   }
 
-  return params;
-}
-
-/**
- * #3513: read stdin into an op's stdin-capable param without ever blocking
- * forever. The old inline `readFileSync(0)` in parseOpArgs assumed non-TTY
- * implies piped content; a non-TTY stdin with NO input (CI step, cron job,
- * agent harness holding an unwritten pipe open) blocked the read until kill.
- *
- * Strategy by fd kind (fstat):
- *  - TTY: skip, as before (interactive input is not an op-param source).
- *  - regular file / /dev/null / anything not a pipe or socket: readFileSync
- *    returns without blocking (`gbrain put x < file`, `< /dev/null` → '').
- *  - FIFO/socket: stream-read with a deadline on the FIRST byte only. A real
- *    pipe (`echo foo | gbrain put x`, heredocs) delivers its first byte
- *    within milliseconds; once any data arrives the deadline is lifted and
- *    we read to EOF like readFileSync did (slow producers stay supported).
- *    An empty-but-closed pipe (`: | gbrain put x`) EOFs immediately → ''.
- *    A pipe that never delivers a byte times out → param stays unset, so
- *    the existing required-param usage error fires (fail fast, exit 1).
- *
- * GBRAIN_STDIN_TIMEOUT_MS overrides the first-byte deadline (default 5000).
- * Exported for tests; called by the op dispatch right after parseOpArgs.
- */
-export async function applyStdinParam(
-  op: Operation,
-  params: Record<string, unknown>,
-): Promise<void> {
-  // Branch shape (stdin hint + missing param + `!process.stdin.isTTY` gate +
-  // 5MB cap) is pinned by the R4 regression test for PR #1325's Windows fix
-  // (test/cycle/regression-pr-wave-r1-r2-r4.test.ts) — keep the spelling.
+  // Read stdin for content params
   if (op.cliHints?.stdin && !params[op.cliHints.stdin] && !process.stdin.isTTY) {
-    const content = await readStdinBounded();
-    if (content === null) return; // no input arrived — let the required-param check fail fast
+    const stdinContent = readFileSync(0, 'utf-8');
     const MAX_STDIN = 5_000_000; // 5MB
-    if (Buffer.byteLength(content, 'utf-8') > MAX_STDIN) {
+    if (Buffer.byteLength(stdinContent, 'utf-8') > MAX_STDIN) {
       console.error(`Error: stdin content exceeds ${MAX_STDIN} bytes. Split into smaller inputs.`);
       process.exit(1);
     }
-    params[op.cliHints.stdin] = content;
+    params[op.cliHints.stdin] = stdinContent;
   }
-}
 
-/** First-byte deadline for pipe/socket stdin (#3513). Env-overridable escape hatch. */
-function stdinFirstByteTimeoutMs(): number {
-  const n = Number(process.env.GBRAIN_STDIN_TIMEOUT_MS);
-  return Number.isFinite(n) && n > 0 ? n : 5000;
-}
-
-/**
- * Returns the full stdin content, '' for a readable-but-empty stdin, or
- * null when stdin is a pipe/socket that never delivered a byte within the
- * first-byte deadline (or the fd is closed/unreadable).
- */
-export async function readStdinBounded(): Promise<string | null> {
-  let isPipeOrSocket: boolean;
-  try {
-    const st = fstatSync(0);
-    isPipeOrSocket = st.isFIFO() || st.isSocket();
-  } catch {
-    return null; // closed/invalid fd — treat as no input
-  }
-  if (!isPipeOrSocket) {
-    // Regular file redirect, /dev/null, etc. — read returns without blocking.
-    try {
-      return readFileSync(0, 'utf-8');
-    } catch {
-      return null;
-    }
-  }
-  return await new Promise<string | null>((resolve) => {
-    const chunks: Buffer[] = [];
-    let gotData = false;
-    const timer = setTimeout(() => {
-      if (!gotData) {
-        process.stdin.destroy();
-        resolve(null);
-      }
-    }, stdinFirstByteTimeoutMs());
-    const finish = () => {
-      clearTimeout(timer);
-      resolve(Buffer.concat(chunks).toString('utf-8'));
-    };
-    process.stdin.on('data', (c: Buffer) => {
-      if (!gotData) {
-        gotData = true;
-        clearTimeout(timer); // deadline applies to the FIRST byte only
-      }
-      chunks.push(c);
-    });
-    process.stdin.once('end', finish);
-    process.stdin.once('error', finish);
-  });
+  return params;
 }
 
 /**
@@ -963,34 +866,20 @@ export function applyThinClientSourceScope(
   params.source_id = resolved;
 }
 
-// Exported for tests (same import-safety contract as applyThinClientSourceScope).
-export async function makeContext(engine: BrainEngine, params: Record<string, unknown>): Promise<OperationContext> {
+async function makeContext(engine: BrainEngine, params: Record<string, unknown>): Promise<OperationContext> {
   // v0.31.8 (D11): resolve sourceId via the canonical 6-tier chain. Honors
   // --source / GBRAIN_SOURCE / .gbrain-source / path-match / brain default /
   // 'default'. Wrapped in try/catch so a doctor / single-source brain that
   // never set up sources still returns 'default' silently.
   let sourceId: string | undefined;
-  // #2561: when the source resolved via a NON-explicit tier (path-match /
-  // brain default / sole-non-default / seed default), unqualified search-shaped
-  // reads span every `config.federated = true` source. Computed here (the
-  // trusted local boundary) and consumed by federatedSearchScope in
-  // operations.ts, which additionally gates on ctx.remote === false.
-  let localFederated: string[] | undefined;
-  // params.source is set when a CLI flag was parsed for the op (rare; most
-  // CLI ops don't take --source). Falls through to env/dotfile/path-match.
-  const explicit = (params.source as string | undefined) ?? null;
   try {
-    const { resolveSourceWithTier, localFederatedSourceIds } = await import('./core/source-resolver.ts');
-    const resolved = await resolveSourceWithTier(engine, explicit);
-    sourceId = resolved.source_id;
-    localFederated = await localFederatedSourceIds(engine, resolved.source_id, resolved.tier);
-  } catch (err) {
-    // #1712: an EXPLICIT --source that fails to resolve (invalid id, or a
-    // source that doesn't exist) must error loudly — the blanket swallow
-    // turned `--source __all__` and typos into a silent `default` scope,
-    // which is how three bug reports became debugging sessions.
-    if (explicit) throw err;
-    // Ambient resolution failed (e.g. sources table doesn't exist on a fresh
+    const { resolveSourceId } = await import('./core/source-resolver.ts');
+    // params.source is set when a CLI flag was parsed for the op (rare; most
+    // CLI ops don't take --source). Falls through to env/dotfile/path-match.
+    const explicit = (params.source as string | undefined) ?? null;
+    sourceId = await resolveSourceId(engine, explicit);
+  } catch {
+    // Source resolution failed (e.g. sources table doesn't exist on a fresh
     // pre-init brain). Leave sourceId unset; engine read methods fall through
     // to the cross-source view (D16 back-compat path).
     sourceId = undefined;
@@ -1009,7 +898,6 @@ export async function makeContext(engine: BrainEngine, params: Record<string, un
     // table). Matches dispatch.ts's auto-fill so the contract holds across
     // every transport.
     sourceId: sourceId ?? 'default',
-    ...(localFederated ? { localFederatedSourceIds: localFederated } : {}),
   };
 }
 
@@ -1111,10 +999,7 @@ export function formatResult(opName: string, result: unknown): string {
         lines.push(`Link coverage (entities): ${(h.link_coverage * 100).toFixed(1)}%`);
       }
       if (h.timeline_coverage !== undefined) {
-        lines.push(`Timeline coverage (entity pages): ${(h.timeline_coverage * 100).toFixed(1)}%`);
-      }
-      if (h.timeline_coverage_score !== undefined) {
-        lines.push(`Timeline density (all pages): ${h.timeline_coverage_score}/15 (whole-brain brain-score component)`);
+        lines.push(`Timeline coverage (entities): ${(h.timeline_coverage * 100).toFixed(1)}%`);
       }
       if (Array.isArray(h.most_connected) && h.most_connected.length > 0) {
         lines.push('Most connected entities:');
@@ -1156,7 +1041,7 @@ export function formatResult(opName: string, result: unknown): string {
  * `runRemoteDoctor` for thin-client installs.
  */
 const THIN_CLIENT_REFUSED_COMMANDS = new Set([
-  'sync', 'embed', 'extract', 'extract-conversation-facts', 'enrich', 'migrate', 'retrieval-upgrade', 'apply-migrations',
+  'sync', 'embed', 'extract', 'extract-conversation-facts', 'enrich', 'migrate', 'apply-migrations',
   'repair-jsonb', 'orphans', 'integrity', 'serve',
   // v0.43 (#2095): watch streams against a LOCAL engine; thin clients get
   // the volunteer_context MCP op instead.
@@ -1203,7 +1088,6 @@ const THIN_CLIENT_REFUSE_HINTS: Record<string, string> = {
   'extract-conversation-facts': 'extract-conversation-facts runs on the host (requires local engine + chat gateway). Run on the host machine.',
   enrich: 'enrich runs on the host (requires local engine + chat gateway for grounded synthesis). Run on the host machine.',
   migrate: "migrate runs on the host's local engine. Run on the host machine.",
-  'retrieval-upgrade': "retrieval-upgrade (embedding migration) rebuilds the host brain's schema + re-embeds. Run on the host machine.",
   'apply-migrations': 'schema migrations run on the host. SSH and run there.',
   'repair-jsonb': 'repair-jsonb operates on the local DB only.',
   integrity: 'integrity scans local files. Run on the host machine.',
@@ -1270,20 +1154,6 @@ async function handleCliOnly(command: string, args: string[]) {
     await runInit(args);
     return;
   }
-  if (command === 'bench') {
-    // #3502 sweep: `gbrain bench publish` was documented (docs/eval-bench.md,
-    // KEY_FILES.md, and eval-gate's own --help text) but never dispatched —
-    // the promised-but-unwired class retrieval-upgrade (#3390) fixed before.
-    // Pure file-in/file-out (NDJSON → baseline); no DB, no engine.
-    if (args[0] === 'publish') {
-      const { runBenchPublish } = await import('./commands/bench-publish.ts');
-      await runBenchPublish(args.slice(1));
-      return;
-    }
-    console.error('Usage: gbrain bench publish --from <captured.ndjson> --to <X.baseline.ndjson> [flags]');
-    console.error('Run `gbrain bench publish --help` for the full flag list.');
-    process.exit(args[0] === '--help' || args[0] === '-h' ? 0 : 2);
-  }
   // v0.37 fix wave (deferred TODO, shipped): one-command wipe-and-reinit.
   // Spawns its own engine internally so no pre-bound engine needed.
   if (command === 'reinit-pglite') {
@@ -1868,33 +1738,10 @@ async function handleCliOnly(command: string, args: string[]) {
       }
       // doctor is handled before connectEngine() above
       case 'migrate': {
-        // #3390: `gbrain migrate embeddings --to <provider:model>` — the
-        // provider-agnostic embedding migration. Everything else stays the
-        // engine-transfer path (`migrate --to <supabase|pglite>`).
-        if (args[0] === 'embeddings') {
-          const { runMigrateEmbeddings } = await import('./commands/migrate-embeddings.ts');
-          await runMigrateEmbeddings(engine, args.slice(1));
-          break;
-        }
-        if (args.includes('--help') || args.includes('-h')) {
-          console.log('Usage: gbrain migrate --to <supabase|pglite> [--url <url>] [--path <path>] [--force]');
-          console.log('       gbrain migrate embeddings --to <provider:model> [--dim N] [--dry-run] [--yes]');
-          console.log('');
-          console.log('The first form transfers the brain between engines; the second re-embeds');
-          console.log('onto a different embedding provider (run `gbrain migrate embeddings --help`).');
-          break;
-        }
         const { runMigrateEngine } = await import('./commands/migrate-engine.ts');
         await runMigrateEngine(engine, args);
         break;
       }
-      case 'retrieval-upgrade': {
-        // The command README.md + doctor.ts promised since v0.36 but never
-        // dispatched. Alias for `migrate embeddings` (#3390).
-        const { runMigrateEmbeddings } = await import('./commands/migrate-embeddings.ts');
-        await runMigrateEmbeddings(engine, args);
-        break;
-      }
       case 'eval': {
         // v0.32 EXP-5: `eval takes-quality {run,trend,regress}` requires a
         // brain (samples takes from DB / reads runs table). `replay` was
@@ -1974,11 +1821,6 @@ async function handleCliOnly(command: string, args: string[]) {
         await runOrphans(engine, args);
         break;
       }
-      case 'maintain': {
-        const { runMaintain } = await import('./commands/maintain.ts');
-        await runMaintain(engine, args);
-        break;
-      }
       // v0.32.7 CJK wave — post-upgrade markdown re-chunk sweep.
       // v0.36 Phase 3 wave — `gbrain reindex --multimodal` re-embeds content_chunks
       // into the unified Voyage multimodal-3 column.
@@ -2491,7 +2333,6 @@ USAGE
 SETUP
   init [--pglite|--supabase|--url]   Create brain (PGLite default, no server)
   migrate --to <supabase|pglite>     Transfer brain between engines
-  migrate embeddings --to <p:model>  Re-embed onto another embedding provider
   upgrade                            Self-update
   check-update [--json]              Check for new versions
   doctor [--json] [--fast]            Health check (resolver, skills, pgvector, RLS, embeddings)
@@ -2513,8 +2354,6 @@ IMPORT/EXPORT
   sync [--repo <path>] [flags]       Git-to-brain incremental sync
   sync --watch [--interval N]        Continuous sync (loops until stopped)
                                      See also: autopilot --install (continuous daemon).
-  sync --all --missing-path skip     Classify sources whose local_path is absent
-                                     on this machine as skipped, not failed
   export [--dir ./out/]              Export to markdown
   export --restore-only [--repo <p>] Restore missing supabase-only files
         [--type T] [--slug-prefix S] With optional filters
@@ -2559,7 +2398,6 @@ TOOLS
   publish <page.md> [--password]     Shareable HTML (strips private data, optional AES-256)
   check-backlinks <check|fix> [dir]  Find/fix missing back-links across brain
   lint <dir|file> [--fix]            Catch LLM artifacts, placeholder dates, bad frontmatter
-  backfill <kind|list>               v0.30.1: run a registered backfill (effective-date, ...)
   orphans [--json] [--count]         Find pages with no inbound wikilinks
   salience [--days N] [--kind P]     v0.29: pages ranked by emotional + activity salience
   anomalies [--since D] [--sigma N]  v0.29: cohort-based statistical anomalies (tag, type)

src/commands/agent.ts

@@ -66,9 +66,7 @@ USAGE
 SUBMITTING
   gbrain agent run <prompt>
     --subagent-def <name>        Named plugin subagent (from GBRAIN_PLUGIN_PATH)
-    --model <id>                 Model id as provider:model (default: subagent tier model,
-                                  anthropic:claude-sonnet-4-6). Non-Anthropic providers need
-                                  agent.use_gateway_loop enabled — see NOTES below.
+    --model <id>                 Anthropic model id (defaults to sonnet)
     --max-turns <n>              Max assistant turns (default 20)
     --tools a,b,c                Subset of registered tool names (comma list)
     --timeout-ms <n>             Per-job wall-clock timeout
@@ -89,22 +87,9 @@ VIEWING
     --since <spec>               ISO-8601 timestamp OR relative ("5m","1h","2d")
 
 NOTES
-  This CLI path is trusted-only. (Remote MCP callers reach subagents through
-  the scoped submit_agent operation, not through this command.)
-
-  By default the worker runs the legacy Anthropic-direct path, which needs an
-  Anthropic key — from ANTHROPIC_API_KEY or from anthropic_api_key in
-  ~/.gbrain/config.json — or the first LLM turn of a claimed job fails.
-
-  To run --model on a non-Anthropic provider, enable the provider-neutral
-  gateway loop first, then supply whatever credential that provider needs
-  (an API key for most; some recipes use OAuth or a local endpoint):
-    gbrain config set agent.use_gateway_loop true
-  Accepted values: true / 1 / yes / on.
-
-  The gateway loop needs a provider whose recipe supports chat WITH tool
-  calling — not every recipe under src/core/ai/recipes/ qualifies. A model
-  that cannot call tools is refused at job start with the reason named.
+  Submitting subagent jobs is trusted-only; MCP submitters receive
+  permission_denied. The worker needs ANTHROPIC_API_KEY set, or the
+  first LLM turn of a claimed job fails.
 `);
 }
 

src/commands/apply-migrations.ts

@@ -133,15 +133,14 @@ function indexCompleted(entries: CompletedMigrationEntry[]): CompletedIndex {
  * Returns the resolved status for a migration based on its entries.
  *
  * Semantics (Bug 3 — keep "complete wins" safety):
- *   - If the latest entry is `retry`, the version is pending. This is the
- *     explicit escape hatch written by `--force-retry`, and it overrides an
- *     earlier `complete` entry without hand-editing the ledger.
- *   - Otherwise, if any entry is `complete`, the version is complete.
+ *   - If any entry is `complete`, the version is complete. Terminal state.
+ *   - Otherwise, if the latest entry is `retry`, the version is pending
+ *     (user requested a fresh attempt).
  *   - Otherwise, if any entry is `partial`, the version is partial.
  *   - Otherwise, pending.
  *
- * `complete` never regresses accidentally. A later `partial` append cannot
- * undo a completed migration; only a trailing, explicit `retry` marker can.
+ * `complete` never regresses. A later accidental `partial` append cannot
+ * undo a completed migration.
  */
 function statusForVersion(
   version: string,
@@ -149,9 +148,9 @@ function statusForVersion(
 ): 'complete' | 'partial' | 'pending' | 'wedged' {
   const entries = idx.byVersion.get(version) ?? [];
   if (entries.length === 0) return 'pending';
+  if (entries.some(e => e.status === 'complete')) return 'complete';
   const latest = entries[entries.length - 1];
   if (latest.status === 'retry') return 'pending';
-  if (entries.some(e => e.status === 'complete')) return 'complete';
   // Bug 3 attempt cap — count consecutive partials from the end (stopping
   // at any 'retry' or 'complete'). If we hit MAX_CONSECUTIVE_PARTIALS,
   // the migration is wedged and needs explicit --force-retry to try again.
@@ -439,13 +438,6 @@ export async function runApplyMigrations(args: string[]): Promise<void> {
       const result = await m.orchestrator(orchestratorOptsFrom(cli));
       if (result.status === 'failed') {
         console.error(`Migration v${m.version} reported status=failed.`);
-        // Surface each failed phase's detail — the ledger records it, but
-        // the operator needs it on stderr to act (#921).
-        for (const p of result.phases) {
-          if (p.status === 'failed') {
-            console.error(`  phase ${p.name}: ${p.detail ?? '(no detail)'}`);
-          }
-        }
         // Record the attempt as 'partial' (not 'complete') so the cap counts
         // it. Don't let a failed orchestrator look like it never ran.
         try {

src/commands/auth.ts

@@ -515,60 +515,6 @@ async function registerClient(name: string, args: string[]) {
   }
 }
 
-/**
- * v0.42.x (#1914): rescope an existing OAuth client's write source and/or
- * federated read scope. This is the operator surface the DCR registration
- * comment promised ("rescope via the CLI later") — DCR clients land with
- * source_id='default' / federated_read=['default'] and must not self-widen,
- * so widening happens here (trusted local CLI) or via the requireAdmin
- * /admin/api/rescope-client endpoint.
- */
-async function rescopeClient(clientId: string, args: string[]) {
-  const usage = 'Usage: auth rescope-client <client_id> [--source SOURCE] [--federated-read SRC1,SRC2,...]';
-  if (!clientId) {
-    console.error(usage);
-    process.exit(1);
-  }
-  let sourceId: string | undefined;
-  let federatedRead: string[] | undefined;
-  for (let i = 0; i < args.length; i += 2) {
-    const flag = args[i];
-    const value = args[i + 1];
-    if (value === undefined || value.startsWith('--')) {
-      console.error(`Error: ${flag} requires a value`);
-      console.error(usage);
-      process.exit(1);
-    }
-    if (flag === '--source') sourceId = value;
-    else if (flag === '--federated-read') {
-      federatedRead = value.split(',').map(s => s.trim()).filter(Boolean);
-    } else {
-      console.error(`Error: Unknown flag: ${flag}`);
-      console.error(usage);
-      process.exit(1);
-    }
-  }
-  if (sourceId === undefined && federatedRead === undefined) {
-    console.error('Error: pass --source and/or --federated-read');
-    console.error(usage);
-    process.exit(1);
-  }
-  try {
-    await withConfiguredSql(async (sql) => {
-      const { GBrainOAuthProvider } = await import('../core/oauth-provider.ts');
-      const provider = new GBrainOAuthProvider({ sql });
-      const result = await provider.rescopeClient(clientId, { sourceId, federatedRead });
-      console.log(`OAuth client rescoped: "${result.clientName}" (${result.clientId})\n`);
-      console.log(`  Write source:        ${result.sourceId}`);
-      console.log(`  Federated reads:     ${result.federatedRead.join(', ') || '<none>'}`);
-      console.log('\nTakes effect on the client\'s next request (existing tokens included).');
-    });
-  } catch (e: any) {
-    console.error('Error:', e.message);
-    process.exit(1);
-  }
-}
-
 /**
  * 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`
@@ -610,7 +556,6 @@ export async function runAuth(args: string[]): Promise<void> {
       return;
     }
     case 'register-client': await registerClient(rest[0], rest.slice(1)); return;
-    case 'rescope-client': await rescopeClient(rest[0], rest.slice(1)); return;
     case 'revoke-client': await revokeClient(rest[0]); return;
     case 'test': {
       const tokenIdx = rest.indexOf('--token');
@@ -648,11 +593,6 @@ Usage:
      --bound-slug-prefixes <prefix1,prefix2>               Bind submit_agent writes to slug prefixes
      --bound-max-concurrent <n>                            Bound submit_agent concurrency (default: 1)
      --budget-usd-per-day <usd>                            Bound submit_agent daily spend cap
-  gbrain auth rescope-client <client_id> [options]        Change an existing client's source scope (e.g. a DCR
-                                                          client stuck on the 'default' source). Only the flags
-                                                          you pass change; the other axis is left as-is.
-     --source <id>                                        New write source
-     --federated-read <id1,id2,...>                       New read-scope source list
   gbrain auth revoke-client <client_id>                   Hard-delete an OAuth 2.1 client (cascades to tokens + codes)
   gbrain auth test <url> --token <token>                  Smoke-test a remote MCP server
 `);

src/commands/autopilot-timeout.ts

@@ -1,9 +0,0 @@
-export function resolveAutopilotDispatchTimeoutMs(
-  baseIntervalSeconds: number,
-  fullCycle: boolean,
-): number {
-  const intervalDerivedTimeoutMs = Math.max(baseIntervalSeconds * 2 * 1000, 300_000);
-  return fullCycle
-    ? Math.max(intervalDerivedTimeoutMs, 1_800_000)
-    : intervalDerivedTimeoutMs;
-}

src/commands/autopilot.ts

@@ -19,7 +19,7 @@
 
 import { existsSync, readFileSync, writeFileSync, mkdirSync, appendFileSync, utimesSync, unlinkSync, chmodSync } from 'fs';
 import { setCliExitVerdict } from '../core/cli-force-exit.ts';
-import { join, dirname } from 'path';
+import { join } from 'path';
 import { execSync } from 'child_process';
 import type { BrainEngine } from '../core/engine.ts';
 import { loadPreferences } from '../core/preferences.ts';
@@ -38,8 +38,6 @@ import { logSelfUpgrade } from '../core/audit/self-upgrade-audit.ts';
 import { detectInstallMethod } from './upgrade.ts';
 import { evaluateQuietHours } from '../core/minions/quiet-hours.ts';
 import { inspectLock } from '../core/db-lock.ts';
-import { registerCleanup } from '../core/process-cleanup.ts';
-import { resolveAutopilotDispatchTimeoutMs } from './autopilot-timeout.ts';
 
 /**
  * v0.37.7.0 #1162 — classify autopilot reconnect-loop errors.
@@ -435,37 +433,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
   let stopping = false;
   let childSupervisor: ChildWorkerSupervisor | null = null;
 
-  // #1872: graceful engine shutdown. On PGLite the cycle steps run INLINE in
-  // this process, so a hard `process.exit` mid-write (systemctl stop →
-  // SIGTERM) kills WASM Postgres with the WAL dirty and can corrupt the
-  // brain. Two exit paths must both close the engine:
-  //   - autopilot's own shutdown() below (owns SIGINT + internal stops like
-  //     max_crashes / cycle-failure-cap), and
-  //   - process-cleanup's SIGTERM handler (installed at cli.ts module load;
-  //     it runs the cleanup registry with a 3s deadline and then exits) —
-  //     which is why closeEngine is ALSO registered there.
-  // closeEngine aborts the in-flight inline cycle (runCycle checks the
-  // signal between phases and threads it into phase sub-work), gives it a
-  // short bounded window to wind down, then disconnects. PGLite's
-  // disconnect() drains the pending query and checkpoints before closing;
-  // a second call is a no-op (disconnect snapshots + nulls the handle), so
-  // both paths firing is safe.
-  const shutdownAbort = new AbortController();
-  let inflightInlineCycle: Promise<unknown> | null = null;
-  const closeEngine = async () => {
-    shutdownAbort.abort(new Error('autopilot shutdown'));
-    if (inflightInlineCycle) {
-      // ponytail: 2s cap keeps us inside process-cleanup's 3s deadline; a
-      // between-phase abort resolves instantly, a mid-phase one may not.
-      await Promise.race([
-        inflightInlineCycle.catch(() => { /* cycle errors already logged by the loop */ }),
-        new Promise((r) => setTimeout(r, 2_000)),
-      ]);
-    }
-    try { await engine.disconnect(); } catch { /* best-effort */ }
-  };
-  const deregisterEngineClose = registerCleanup('autopilot-engine-close', closeEngine);
-
   if (spawnManagedWorker) {
     const cliPath = resolveGbrainCliPath();
     // Cgroup-aware auto-sized RSS watchdog cap (issue #1678). The old flat
@@ -553,10 +520,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         childSupervisor.killChild('SIGKILL');
       }
     }
-    // #1872: abort the in-flight inline cycle and close the engine BEFORE
-    // process.exit — a hard exit mid-write corrupts PGLite's WASM Postgres.
-    await closeEngine();
-    deregisterEngineClose();
     try { unlinkSync(lockPath); } catch { /* already gone */ }
     process.exit(0);
   };
@@ -564,9 +527,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
   process.on('SIGINT',  () => { void shutdown('SIGINT'); });
 
   let consecutiveErrors = 0;
-  // Parser-probe fixture warning is once-per-process, not once-per-cycle
-  // (compiled-binary installs have no source tree; don't spam the log).
-  let parserProbeFixtureWarned = false;
   // v0.37.7.0 #1162 — counter for consecutive reconnect failures.
   // Reset on every successful health probe or reconnect. Threshold
   // controlled by GBRAIN_AUTOPILOT_MAX_RECONNECT_FAILS env (default 30).
@@ -729,7 +689,7 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         const queue = new MinionQueue(engine);
         const slotMs = Math.floor(Date.now() / (baseInterval * 1000)) * baseInterval * 1000;
         const slot = new Date(slotMs).toISOString();
-        const timeoutMs = resolveAutopilotDispatchTimeoutMs(baseInterval, false);
+        const timeoutMs = Math.max(baseInterval * 2 * 1000, 300_000);
 
         // ── v0.40 D17: per-source freshness check ────────────────────
         // Runs first; independent of score gate. Submits a 'sync' job per
@@ -865,10 +825,7 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
                         {
                           queue: 'default',
                           idempotency_key: idemKey,
-                          // issue #3218: the handler now throws on an
-                          // all-provider-failed batch, so give the queue's
-                          // backoff a chance (was 1 — dead-lettered instantly).
-                          max_attempts: 3,
+                          max_attempts: 1,
                           timeout_ms: timeoutMs,
                         },
                         { allowProtectedSubmit: true },
@@ -908,19 +865,9 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
         } catch {
           embeddingModel = (await engine.getConfig('embedding_model')) ?? undefined;
         }
-        // #2662 (codex round-3): HOSTED_EMBED_KEY_CONFIG entries are keys
-        // buildGatewayConfig folds from the FILE plane only — `gbrain config
-        // set <key> X` writes the DB plane, which never reaches the gateway
-        // for these fields. Reading via engine.getConfig() here (DB plane)
-        // would report a provider "configured" from a DB-only key that the
-        // gateway can never actually use, dispatching a doomed embed job.
-        // Read the same file-plane source context.ts (doctor) reads instead,
-        // so autopilot and doctor agree with what the gateway can see.
-        const { loadConfigFileOnly } = await import('../core/config.ts');
-        const fileCfg = loadConfigFileOnly() as Record<string, unknown> | null;
-        const embedKeyCfg: Record<string, unknown> = {};
+        const embedKeyCfg: Record<string, string | null> = {};
         for (const field of Object.values(HOSTED_EMBED_KEY_CONFIG)) {
-          embedKeyCfg[field] = fileCfg?.[field];
+          embedKeyCfg[field] = await engine.getConfig(field);
         }
         const ctx = {
           repoPath,
@@ -984,9 +931,7 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
           const result = await dispatchPerSource(engine, queue, {
             repoPath,
             slot,
-            // Full cycles can outlive short daemon intervals. Keep lighter dispatches
-            // interval-derived while giving per-source consolidation enough time.
-            timeoutMs: resolveAutopilotDispatchTimeoutMs(baseInterval, true),
+            timeoutMs,
             fanoutMax,
             jsonMode,
           });
@@ -1063,21 +1008,16 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       // path's phase set). Now both converge on the same primitive.
       try {
         const { runCycle } = await import('../core/cycle.ts');
-        // #1872: track the promise so closeEngine can drain it on shutdown,
-        // and pass the abort signal so the cycle winds down between phases.
-        const cyclePromise = runCycle(engine, {
+        const report = await runCycle(engine, {
           brainDir: repoPath,
           // Autopilot daemon path: pulls by default (matches
           // pre-v0.17 autopilot behavior). CLI dream defaults false
           // for cron safety; that choice is scoped to dream only.
           pull: true,
-          signal: shutdownAbort.signal,
           yieldBetweenPhases: async () => {
             await new Promise(r => setImmediate(r));
           },
         });
-        inflightInlineCycle = cyclePromise;
-        const report = await cyclePromise.finally(() => { inflightInlineCycle = null; });
         // Only 'failed' (every attempted phase failed) trips the autopilot
         // circuit breaker. 'partial' means at least one phase warned or
         // failed while others ran — that's a soft signal, not a fatal
@@ -1133,36 +1073,17 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
     // loop. Probe runs even when cycleOk=false (probe may surface signal
     // explaining why the cycle is failing).
     try {
-      const { resolveProbeEnabled, resolveProbeMaxUsd, runNightlyQualityProbe } = await import('../core/cycle/nightly-quality-probe.ts');
-      // Dual-plane read: `gbrain config set` (what the doctor enable hint
-      // prints) writes the DB plane; ~/.gbrain/config.json is the fallback.
-      let dbEnabled: string | null = null;
-      let dbMaxUsd: string | null = null;
-      try {
-        dbEnabled = await engine.getConfig('autopilot.nightly_quality_probe.enabled');
-        dbMaxUsd = await engine.getConfig('autopilot.nightly_quality_probe.max_usd');
-      } catch { /* DB unavailable → file plane only */ }
-      const probeEnabled = resolveProbeEnabled(dbEnabled, cfg?.autopilot?.nightly_quality_probe?.enabled);
+      const probeEnabled = cfg?.autopilot?.nightly_quality_probe?.enabled === true;
       if (probeEnabled) {
+        const { runNightlyQualityProbe } = await import('../core/cycle/nightly-quality-probe.ts');
         const { runLongMemEvalForProbe, runCrossModalBatchForProbe } = await import('../core/cycle/nightly-probe-adapters.ts');
         const { isAvailable } = await import('../core/ai/gateway.ts');
-        const { existsSync } = await import('node:fs');
-        const { fileURLToPath } = await import('node:url');
-        const { join } = await import('node:path');
-        const maxUsd = resolveProbeMaxUsd(dbMaxUsd, cfg?.autopilot?.nightly_quality_probe?.max_usd);
-        // The committed fixture (test/fixtures/longmemeval-nightly.jsonl)
-        // lives in the gbrain PACKAGE, not the brain repo — repoPath is
-        // sync.repo_path (the user's brain), where the fixture never
-        // exists, so the probe error'd on every real install. Resolve the
-        // package root from the module location; keep repoPath as the
-        // fallback for setups that vendor the fixture into the brain repo.
-        const pkgRoot = fileURLToPath(new URL('../..', import.meta.url));
-        const fixtureAtPkgRoot = existsSync(join(pkgRoot, 'test', 'fixtures', 'longmemeval-nightly.jsonl'));
+        const maxUsd = Number(cfg?.autopilot?.nightly_quality_probe?.max_usd ?? 5);
         await runNightlyQualityProbe({
           isEnabled: () => true, // already gated above; phase re-checks for defense-in-depth
           hasEmbeddingProvider: () => isAvailable('embedding'),
           resolveMaxUsd: () => maxUsd,
-          resolveRepoRoot: () => (fixtureAtPkgRoot ? pkgRoot : repoPath ?? gbrainHomePath('.')),
+          resolveRepoRoot: () => repoPath ?? gbrainHomePath('.'),
           runLongMemEval: runLongMemEvalForProbe,
           runCrossModalBatch: runCrossModalBatchForProbe,
           now: () => new Date(),
@@ -1174,62 +1095,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       // informational; autopilot loop continues.
     }
 
-    // 4.6 — Nightly conversation-parser probe (v0.41.16.0 phase module;
-    // the scheduler wire-up was deferred at ship and is added here). Same
-    // posture as 4.5: the phase owns its gates (enabled/mode-gate, LLM
-    // key), the wiring owns invocation + the audit row, and a probe
-    // failure NEVER crashes the autopilot loop. Per D10 the probe is
-    // default-ON for search.mode=tokenmax, opt-in otherwise.
-    try {
-      const { runConversationParserNightlyProbe } = await import('../core/conversation-parser/nightly-probe.ts');
-      const { logParserProbeEvent, parserProbeRanWithin } = await import('../core/audit-parser-probe.ts');
-      const { isAvailable } = await import('../core/ai/gateway.ts');
-      const { existsSync } = await import('node:fs');
-      const { fileURLToPath } = await import('node:url');
-      const { join } = await import('node:path');
-      // Flag reads dual-plane: the DB row (`gbrain config set …`) wins,
-      // ~/.gbrain/config.json is the fallback. search.mode lives on the
-      // DB plane only (mode.ts owns it).
-      let parserDbEnabled: string | null = null;
-      let dbSearchMode: string | null = null;
-      try {
-        parserDbEnabled = await engine.getConfig('autopilot.conversation_parser_probe.enabled');
-        dbSearchMode = await engine.getConfig('search.mode');
-      } catch { /* DB unavailable → file plane only */ }
-      const parserEnabled = parserDbEnabled != null
-        ? parserDbEnabled === 'true'
-        : cfg?.autopilot?.conversation_parser_probe?.enabled === true;
-      const searchMode = dbSearchMode ?? '';
-      // Fixtures are committed in the gbrain package (test/fixtures/…),
-      // NOT the brain repo — resolve from the module location. Compiled
-      // binaries carry no source tree: skip quietly instead of writing
-      // failure rows that would flip doctor to WARN on every binary install.
-      const pkgRoot = fileURLToPath(new URL('../..', import.meta.url));
-      const fixturePath = join(pkgRoot, 'test', 'fixtures', 'conversation-formats', 'all.jsonl');
-      const adversarialPath = join(pkgRoot, 'test', 'fixtures', 'conversation-formats', 'adversarial.jsonl');
-      const shouldInvoke = parserEnabled || searchMode === 'tokenmax';
-      if (shouldInvoke && existsSync(fixturePath) && existsSync(adversarialPath)) {
-        const result = await runConversationParserNightlyProbe({
-          isEnabled: () => parserEnabled,
-          searchMode: () => searchMode,
-          hasLlmKey: () => isAvailable('chat'),
-          resolveFixturePath: () => fixturePath,
-          resolveAdversarialPath: () => adversarialPath,
-          now: () => new Date(),
-          shouldSkipForRateLimit: () => parserProbeRanWithin(24 * 60 * 60 * 1000),
-        });
-        // rate_limited is a non-run: the loop ticks every few minutes, so
-        // logging every skip would flood the audit file with no-signal rows.
-        if (result.outcome !== 'rate_limited') logParserProbeEvent(result);
-      } else if (shouldInvoke && !parserProbeFixtureWarned) {
-        parserProbeFixtureWarned = true;
-        console.error(`[parser-probe] fixtures not found under ${pkgRoot}; skipping (probe needs a source-checkout install)`);
-      }
-    } catch (e) {
-      logError('autopilot.parser_probe', e);
-      // Informational, like 4.5: do NOT bump consecutiveErrors.
-    }
-
     // Wait for next cycle
     await new Promise(r => setTimeout(r, interval * 1000));
   }
@@ -1312,17 +1177,6 @@ function writeWrapperScript(repoPath: string): string {
   const gbrainPath = resolveGbrainCliPath();
   const safeRepoPath = repoPath.replace(/'/g, "'\\''");
   const safeGbrainPath = gbrainPath.replace(/'/g, "'\\''");
-  // Bake the dir of the bun runtime actually executing this install onto PATH,
-  // so the wrapper finds bun wherever it lives — Homebrew (/opt/homebrew/bin),
-  // npm -g, Docker (/usr/local/bin), a custom BUN_INSTALL, or nix — not just
-  // ~/.bun/bin (which #3305 hardcoded, covering only the default bun.sh installer).
-  // dirname('') === '.', so guard the degenerate/empty case — otherwise a missing
-  // execPath would prepend '.' (cwd) onto a cron PATH. Empty prefix falls back to
-  // the #3305 behavior exactly.
-  const runtimeDir = dirname(process.execPath || '');
-  const runtimePathPrefix = runtimeDir && runtimeDir !== '.'
-    ? `'${runtimeDir.replace(/'/g, "'\\''")}':`
-    : '';
   const wrapper = `#!/bin/bash
 # Auto-generated by gbrain autopilot --install
 # Sources shell profile for API keys, then runs autopilot.
@@ -1332,16 +1186,6 @@ function writeWrapperScript(repoPath: string): string {
 # OPENAI/ANTHROPIC keys exported in zshenv reach autopilot.
 [ -f ~/.zshenv ] && source ~/.zshenv 2>/dev/null
 source ~/.zshrc 2>/dev/null || source ~/.bashrc 2>/dev/null || true
-# Belt-and-suspenders PATH fix. ~/.bashrc ships with a non-interactive guard
-# (\`case $- in *i*) ;; *) return;; esac\`) that exits early when launched from
-# cron/systemd/launchd — so its PATH exports never reach this subprocess.
-# Without bun on PATH, the exec'd gbrain (a \`#!/usr/bin/env bun\` script) fails
-# silently with "env: bun: No such file or directory" and leaves a stale
-# lockfile that blocks every subsequent tick. Prepending the running bun's own
-# dir (derived from process.execPath at install time), with ~/.bun/bin kept as a
-# fallback, keeps the wrapper self-contained regardless of where bun is installed
-# or which init file the OS loaded.
-export PATH=${runtimePathPrefix}"$HOME/.bun/bin:$PATH"
 exec '${safeGbrainPath}' autopilot --repo '${safeRepoPath}'
 `;
   writeFileSync(wrapperPath, wrapper, { mode: 0o755 });
@@ -1768,10 +1612,7 @@ function showStatus(json: boolean) {
   } else {
     try {
       const crontab = execSync('crontab -l 2>/dev/null || true', { encoding: 'utf-8' });
-      // The installed cron line invokes the generated wrapper (…/autopilot-run.sh);
-      // older installs called `gbrain autopilot` directly. Match either so status
-      // isn't a false negative after the wrapper indirection landed.
-      installed = crontab.includes('autopilot-run.sh') || crontab.includes('gbrain autopilot');
+      installed = crontab.includes('gbrain autopilot');
     } catch { /* no crontab */ }
   }
 

src/commands/backlinks.ts

@@ -5,8 +5,8 @@
  * checks if back-links exist, and optionally creates them.
  *
  * Usage:
- *   gbrain check-backlinks check [dir] [--dir <brain-dir>] # report missing back-links
- *   gbrain check-backlinks fix [dir] [--dir <brain-dir>]   # create missing back-links
+ *   gbrain check-backlinks check [--dir <brain-dir>]     # report missing back-links
+ *   gbrain check-backlinks fix [--dir <brain-dir>]        # create missing back-links
  *   gbrain check-backlinks fix --dry-run                  # preview fixes
  */
 
@@ -201,40 +201,6 @@ export interface BacklinksResult {
   dryRun: boolean;
 }
 
-export interface ParsedBacklinksArgs {
-  subcommand: string | undefined;
-  brainDir: string;
-  dryRun: boolean;
-}
-
-export function parseBacklinksArgs(args: string[]): ParsedBacklinksArgs {
-  const subcommand = args[0];
-  const dryRun = args.includes('--dry-run');
-  const dirIdx = args.indexOf('--dir');
-  const flagDir = dirIdx >= 0 && args[dirIdx + 1] && !args[dirIdx + 1].startsWith('--')
-    ? args[dirIdx + 1]
-    : undefined;
-
-  let positionalDir: string | undefined;
-  for (let i = 1; i < args.length; i++) {
-    const arg = args[i];
-    if (arg === '--dir') {
-      i++;
-      continue;
-    }
-    if (arg === '--dry-run') continue;
-    if (arg.startsWith('--')) continue;
-    positionalDir = arg;
-    break;
-  }
-
-  return {
-    subcommand,
-    brainDir: flagDir ?? positionalDir ?? '.',
-    dryRun,
-  };
-}
-
 /**
  * Library-level backlinks check/fix. Throws on validation errors; returns a
  * structured result so Minions handlers + autopilot-cycle can surface counts.
@@ -270,14 +236,16 @@ export async function runBacklinksCore(opts: BacklinksOpts): Promise<BacklinksRe
 }
 
 export async function runBacklinks(args: string[]) {
-  const { subcommand, brainDir, dryRun } = parseBacklinksArgs(args);
+  const subcommand = args[0];
+  const dirIdx = args.indexOf('--dir');
+  const brainDir = dirIdx >= 0 ? args[dirIdx + 1] : '.';
+  const dryRun = args.includes('--dry-run');
 
   if (!subcommand || !['check', 'fix'].includes(subcommand)) {
-    console.error('Usage: gbrain check-backlinks <check|fix> [dir] [--dir <brain-dir>] [--dry-run]');
+    console.error('Usage: gbrain check-backlinks <check|fix> [--dir <brain-dir>] [--dry-run]');
     console.error('  check    Report missing back-links');
     console.error('  fix      Create missing back-links (appends to Timeline)');
-    console.error('  dir      Brain directory (default: current directory)');
-    console.error('  --dir    Brain directory override');
+    console.error('  --dir    Brain directory (default: current directory)');
     console.error('  --dry-run  Preview fixes without writing');
     process.exit(1);
   }

src/commands/calibration.ts

@@ -23,7 +23,6 @@ import { runPhaseCalibrationProfile } from '../core/cycle/calibration-profile.ts
 import { sourceScopeOpts, type OperationContext } from '../core/operations.ts';
 import type { GBrainConfig } from '../core/config.ts';
 import { GBrainError } from '../core/types.ts';
-import { resolveOwnerHolder } from '../core/owner-holder.ts';
 
 export interface CalibrationProfileRow {
   /** BIGSERIAL → string (postgres.js int8 wire shape; never Number() — int8
@@ -168,10 +167,7 @@ export async function runCalibration(
   config: GBrainConfig,
 ): Promise<void> {
   const { opts } = parseArgs(args);
-  const holder = resolveOwnerHolder({
-    override: opts.holder,
-    configValue: await engine.getConfig('emotional_weight.user_holder'),
-  });
+  const holder = opts.holder ?? 'garry';
   // Resolve --source / GBRAIN_SOURCE / .gbrain-source so the (now reachable, #2035)
   // calibration command targets the right source in a multi-source brain instead
   // of always reading `default`. No signal → 'default' (prior behavior).
@@ -257,15 +253,12 @@ export async function getCalibrationProfileOp(
   ctx: OperationContext,
   params: { holder?: string },
 ): Promise<CalibrationProfileRow | null> {
-  const holder = resolveOwnerHolder({
-    override: params.holder,
-    configValue: await ctx.engine.getConfig('emotional_weight.user_holder'),
-  });
+  const holder = params.holder ?? 'garry';
   if (typeof holder !== 'string' || holder.length === 0) {
     throw new GBrainError(
       'INVALID_HOLDER',
       'get_calibration_profile.holder must be a non-empty string',
-      'pass holder="<slug>" or omit to default to the owner holder (config emotional_weight.user_holder, else "self")',
+      'pass holder="<slug>" or omit to default to "garry"',
     );
   }
   const scope = sourceScopeOpts(ctx);

src/commands/capture.ts

@@ -233,18 +233,14 @@ export function maybeRewriteSourceFkError(err: unknown, sourceId: string | undef
 
 /**
  * Derive a title from the first non-empty, non-`---` line of the body,
- * stripping leading markdown heading marks, capped at 80 chars. Truncation
- * is codepoint-aware (never splits an astral surrogate pair) and appends an
- * ellipsis so a cut title is visibly cut.
+ * stripping leading markdown heading marks, capped at 80 chars.
  * Falls back to 'Capture' when no usable line exists.
  */
 function deriveTitle(rawBody: string): string {
   const firstLine = rawBody
     .split('\n')
     .find((l) => l.trim().length > 0 && l.trim() !== '---') ?? '';
-  const stripped = firstLine.replace(/^#+\s*/, '');
-  const cps = [...stripped];
-  return (cps.length > 80 ? cps.slice(0, 79).join('') + '…' : stripped) || 'Capture';
+  return firstLine.replace(/^#+\s*/, '').slice(0, 80) || 'Capture';
 }
 
 /**

src/commands/check-update.ts

@@ -2,13 +2,12 @@ import { VERSION } from '../version.ts';
 import { detectInstallMethod } from './upgrade.ts';
 import {
   isMinorOrMajorBump,
-  isNewerVersion,
   isValidVersionString,
   parseSemver,
   semverGt,
   semverLte,
 } from '../core/semver.ts';
-import { readUpdateCache, writeUpdateCache, type UpdateMarker } from '../core/self-upgrade.ts';
+import { writeUpdateCache, type UpdateMarker } from '../core/self-upgrade.ts';
 
 /** Best-effort cache write — a read-only ~/.gbrain must never make the check throw. */
 function safeWriteCache(marker: UpdateMarker): void {
@@ -22,7 +21,7 @@ function safeWriteCache(marker: UpdateMarker): void {
 // Back-compat re-exports: these used to live here; moved to ../core/semver.ts
 // so the self-upgrade decision module can depend on them without an import
 // cycle. Existing importers (`test/check-update.test.ts`, etc.) keep working.
-export { parseSemver, isMinorOrMajorBump, isNewerVersion };
+export { parseSemver, isMinorOrMajorBump };
 
 interface CheckUpdateResult {
   current_version: string;
@@ -45,53 +44,26 @@ function upgradeCommandForMethod(method: string): string {
   }
 }
 
-/** Where the latest version is resolved from. gbrain publishes NO GitHub
- * releases (the `releases/latest` API is a permanent 404), so the release
- * train's source of truth is the `VERSION` file on master — same trusted host
- * `fetchChangelog` already uses. An npm fallback was rejected: the `gbrain`
- * package on npm is an unrelated GPU library (#505), so it would produce false
- * upgrade prompts pointing at a stranger's package. */
-const VERSION_SOURCE_URL = 'https://raw.githubusercontent.com/garrytan/gbrain/master/VERSION';
-const RELEASE_NOTES_URL = 'https://github.com/garrytan/gbrain/blob/master/CHANGELOG.md';
-
-/** Extract a version from the raw VERSION file body: first line, optional `v`
- * prefix, optional `-suffix` channel tag (`0.31.1.1-fixwave` compares as its
- * numeric base — fail-safe: a suffix-only bump never prompts). Body is bounded
- * before parsing so a malformed/huge response can't blow up the check. */
-export function parseVersionFileBody(body: string): string | null {
-  const firstLine = body.slice(0, 256).trim().split('\n')[0].trim();
-  const m = firstLine.match(/^v?(\d+\.\d+\.\d+(?:\.\d+)?)(?:[-+][0-9A-Za-z.-]+)?$/);
-  return m && isValidVersionString(m[1]) ? m[1] : null;
-}
-
-export type LatestReleaseResult =
-  | { ok: true; tag: string; published_at: string; url: string }
-  | { ok: false; reason: 'network_error' | 'no_releases' };
-
 /**
- * Resolve the latest published gbrain version (from VERSION on master — see
- * VERSION_SOURCE_URL). Exported (v0.42) so the self-upgrade refresh path and
- * tests can reuse it. 5s timeout — this runs on the detached refresh, never the
- * hot path. Failures are discriminated: `network_error` (offline/timeout) vs
- * `no_releases` (endpoint answered but no usable version).
+ * Fetch the latest GitHub release. Exported (v0.42) so the self-upgrade refresh
+ * path and tests can reuse it. 5s timeout (was 10s) — this runs on the detached
+ * refresh, never the hot path, but a tight bound keeps the refresh cheap.
  */
-export async function fetchLatestRelease(): Promise<LatestReleaseResult> {
-  let res: Response;
+export async function fetchLatestRelease(): Promise<{ tag: string; published_at: string; url: string } | null> {
   try {
-    res = await fetch(VERSION_SOURCE_URL, {
+    const res = await fetch('https://api.github.com/repos/garrytan/gbrain/releases/latest', {
       headers: { 'User-Agent': `gbrain/${VERSION}` },
       signal: AbortSignal.timeout(5_000),
     });
+    if (!res.ok) return null;
+    const data = await res.json() as any;
+    return {
+      tag: data.tag_name || '',
+      published_at: data.published_at || '',
+      url: data.html_url || '',
+    };
   } catch {
-    return { ok: false, reason: 'network_error' };
-  }
-  try {
-    if (!res.ok) return { ok: false, reason: 'no_releases' };
-    const tag = parseVersionFileBody(await res.text());
-    if (!tag) return { ok: false, reason: 'no_releases' };
-    return { ok: true, tag, published_at: '', url: RELEASE_NOTES_URL };
-  } catch {
-    return { ok: false, reason: 'network_error' };
+    return null;
   }
 }
 
@@ -145,37 +117,21 @@ export function extractChangelogBetween(changelog: string, from: string, to: str
 }
 
 /**
- * A failed check must NEVER write `up_to_date` — that was #486: the fetch
- * failed permanently (dead releases API) and every user was told "you're
- * current" forever. Instead, re-write the last-known-good marker (bumping its
- * mtime so the cache TTL still throttles retries and a network blip can't
- * erase a pending upgrade_available notice). No prior marker → write nothing;
- * the next invocation retries.
- */
-function preserveCacheOnFailedCheck(): void {
-  try {
-    const prior = readUpdateCache();
-    if (prior) safeWriteCache(prior.marker);
-  } catch {
-    /* best-effort */
-  }
-}
-
-/**
- * Fetch the latest version and write the self-upgrade cache (the marker line
- * read by the CLI startup hook). On fetch failure the last-known-good marker is
- * preserved (see preserveCacheOnFailedCheck) — never a fabricated `up_to_date`.
- * This is the function the detached single-flight refresh (`gbrain
- * check-update --refresh-cache`) invokes.
+ * Fetch the latest release and write the self-upgrade cache (the marker line
+ * read by the CLI startup hook). Fail-open: on any network failure we cache
+ * `UP_TO_DATE <current>` so the TTL prevents hammering GitHub on every
+ * invocation. Returns the resolved marker for callers that want it. This is the
+ * function the detached single-flight refresh (`gbrain check-update
+ * --refresh-cache`) invokes.
  */
 export async function refreshUpdateCache(): Promise<void> {
   const release = await fetchLatestRelease();
-  if (!release.ok) {
-    preserveCacheOnFailedCheck();
+  if (!release) {
+    safeWriteCache({ kind: 'up_to_date', current: VERSION });
     return;
   }
   const latestVersion = release.tag.replace(/^v/, '');
-  if (!isValidVersionString(latestVersion) || !isNewerVersion(VERSION, latestVersion)) {
+  if (!isValidVersionString(latestVersion) || !isMinorOrMajorBump(VERSION, latestVersion)) {
     safeWriteCache({ kind: 'up_to_date', current: VERSION });
     return;
   }
@@ -184,7 +140,7 @@ export async function refreshUpdateCache(): Promise<void> {
 
 export async function runCheckUpdate(args: string[]) {
   if (args.includes('--help') || args.includes('-h')) {
-    console.log('Usage: gbrain check-update [--json] [--refresh-cache]\n\nCheck for new GBrain versions.\n\nReports any strictly newer release, including patch and micro updates.\nFails silently on network errors.\n\n--refresh-cache  Fetch + update the self-upgrade cache, print nothing (used by\n                 the CLI startup hook\'s detached refresh).');
+    console.log('Usage: gbrain check-update [--json] [--refresh-cache]\n\nCheck for new GBrain versions.\n\nOnly reports minor/major version bumps (v0.X.0), not patches.\nFails silently on network errors.\n\n--refresh-cache  Fetch + update the self-upgrade cache, print nothing (used by\n                 the CLI startup hook\'s detached refresh).');
     return;
   }
 
@@ -209,8 +165,9 @@ export async function runCheckUpdate(args: string[]) {
 
   const release = await fetchLatestRelease();
 
-  if (!release.ok) {
-    preserveCacheOnFailedCheck();
+  if (!release) {
+    // Warm the cache fail-open so the startup hook doesn't re-fetch every call.
+    safeWriteCache({ kind: 'up_to_date', current: VERSION });
     if (json) {
       console.log(JSON.stringify({
         current_version: VERSION,
@@ -221,18 +178,16 @@ export async function runCheckUpdate(args: string[]) {
         release_url: '',
         changelog_diff: '',
         published_at: '',
-        error: release.reason,
+        error: 'no_releases',
       }, null, 2));
-    } else if (release.reason === 'network_error') {
-      console.log(`GBrain ${VERSION} — could not check for updates (network unavailable).`);
     } else {
-      console.log(`GBrain ${VERSION} — could not determine the latest published version.`);
+      console.log(`GBrain ${VERSION} — could not check for updates (no releases found or network unavailable).`);
     }
     return;
   }
 
   const latestVersion = release.tag.replace(/^v/, '');
-  const updateAvailable = isValidVersionString(latestVersion) && isNewerVersion(VERSION, latestVersion);
+  const updateAvailable = isValidVersionString(latestVersion) && isMinorOrMajorBump(VERSION, latestVersion);
 
   // Warm the self-upgrade cache so the next `gbrain <cmd>` startup hook can emit
   // the marker without a network call.

src/commands/code-def.ts

@@ -37,19 +37,9 @@ export async function findCodeDef(
   // trigger) are first-class definitions in the SQL sense. The chunker's
   // normalizeSymbolType maps create_table → 'table' etc, so adding the SQL
   // kinds here is what makes `gbrain code-def users` work against SQL.
-  // Method-level + member definitions. normalizeSymbolType only canonicalizes
-  // some node types; the rest fall through `type.replace(/_/g, ' ')`, so
-  // tree-sitter's method_declaration → 'method declaration', struct_specifier →
-  // 'struct specifier', protocol_declaration → 'protocol declaration', etc.
-  // Without these, code-def is blind to every method, constructor, field, C
-  // struct, and Swift protocol — which is most of an OO codebase. The plain
-  // 'struct' entry above never matched for the same reason (C emits the
-  // 'struct specifier' fallback form).
   const DEF_TYPES = [
     'function', 'class', 'interface', 'type', 'enum', 'struct', 'trait', 'module', 'contract',
     'table', 'view', 'index', 'procedure', 'schema', 'database', 'trigger',
-    'method declaration', 'method definition', 'constructor declaration',
-    'field declaration', 'field definition', 'struct specifier', 'protocol declaration',
   ];
   const params: unknown[] = [symbol, limit];
   let whereLang = '';

src/commands/dream.ts

@@ -26,7 +26,6 @@
 import type { BrainEngine } from '../core/engine.ts';
 import {
   runCycle,
-  resolveSourceForDir,
   ALL_PHASES,
   type CyclePhase,
   type CycleReport,
@@ -86,7 +85,7 @@ interface DreamArgs {
    * `--phase <name>`; bare `--once` is a usage error (there'd be no single
    * phase to target). Applies only to phases with a config `.enabled` gate
    * (patterns, synthesize, conversation_facts_backfill, enrich_thin,
-   * skillopt, drift) — a no-op for phases that always run when named directly.
+   * skillopt) — a no-op for phases that always run when named directly.
    */
   once: boolean;
 }
@@ -367,7 +366,7 @@ Options:
                       unlike toggling the flag on/off around the run, a
                       crash mid-invocation can't leave it stuck. Applies to
                       patterns, synthesize, conversation_facts_backfill,
-                      enrich_thin, skillopt, drift; no-op on phases with no such
+                      enrich_thin, skillopt; no-op on phases with no such
                       gate. Requires an EXPLICIT --phase <name> — a phase
                       implied by --input or --drain does not count (bare
                       --once, or --once with --input/--drain and no
@@ -381,9 +380,9 @@ Options:
 
   --source <id>       Scope the cycle to one source so doctor's
                       cycle_freshness check sees a fresh stamp on
-                      completion. When omitted, gbrain derives the
-                      source from --dir / the configured checkout
-                      when it matches a source's local_path (#1869).
+                      completion. Without this, gbrain dream's
+                      timestamp never lands and federated brains
+                      see "stale cycle" forever.
   --source-id <id>    Alias for --source. Matches the v0.37.7.0+
                       naming used by import/extract/graph-query.
 
@@ -635,25 +634,6 @@ export async function runDream(engine: BrainEngine | null, args: string[]): Prom
     );
     process.exit(1);
   }
-
-  // #1869: a path-scoped run (--dir, or the configured sync.repo_path) whose
-  // directory matches a registered source's local_path IS that source's cycle
-  // — derive the source id so runCycle writes last_source_cycle_at /
-  // last_full_cycle_at on success and doctor's cycle_freshness check stops
-  // reading perpetually stale. Explicit --source still wins (resolved above).
-  // Fixed here at the command level, NOT in runCycle's stamp gate, so legacy
-  // global callers (autopilot-global-maintenance runs GLOBAL_PHASES with a
-  // brainDir and no sourceId) can't falsely stamp per-source freshness.
-  // A derived match on an archived source is skipped silently (falls back to
-  // legacy unscoped behavior) — stamping it would mask staleness on restore,
-  // mirroring the explicit --source archived guard above.
-  if (resolvedSourceId === undefined && engine !== null && brainDir !== null) {
-    const derived = await resolveSourceForDir(engine, brainDir);
-    if (derived !== undefined) {
-      const src = await fetchSource(engine, derived);
-      if (src?.archived !== true) resolvedSourceId = derived;
-    }
-  }
   // ─── issue #1678: bounded single-hold extract_atoms drain ──────────
   if (opts.drain) {
     if (engine === null) {

src/commands/embed.ts

@@ -19,26 +19,6 @@ import {
 } from '../core/pace-mode.ts';
 import { tryAcquireDbLock, type DbLockHandle } from '../core/db-lock.ts';
 import { embedBackfillLockId } from '../core/embed-backfill-lock.ts';
-import { wrapChunkTextsForStoredMode } from '../core/embedding-context.ts';
-import { titleTierCorpusGeneration } from '../core/contextual-retrieval-service.ts';
-import type { Page } from '../core/types.ts';
-
-/**
- * #3507 — after a plain re-embed fully re-embedded a `per_chunk_synopsis`
- * page at the title-only tier (see wrapChunkTextsForStoredMode), restamp the
- * page's CR state to 'title' so `contextual_retrieval_mode` keeps describing
- * the vectors actually in the column. The reindex sweep restores the synopsis
- * tier later. No-op for every other mode.
- */
-export async function restampIfDemotedToTitleTier(
-  engine: BrainEngine,
-  page: Pick<Page, 'contextual_retrieval_mode'> | null | undefined,
-  slug: string,
-  sourceId: string,
-): Promise<void> {
-  if (page?.contextual_retrieval_mode !== 'per_chunk_synopsis') return;
-  await engine.updatePageContextualRetrievalState(slug, sourceId, 'title', titleTierCorpusGeneration());
-}
 
 export interface EmbedOpts {
   /** Embed ALL pages (every chunk). */
@@ -127,24 +107,6 @@ export interface EmbedOpts {
    * runs lock every source in sorted order. dryRun skips it.
    */
   singleFlight?: boolean;
-  /**
-   * #394: suppress human stdout summaries (the `[dry-run] Would embed ...` /
-   * `Embedded N chunks ...` slog lines). Set by structured-output callers —
-   * the cycle's embed phase (dream --json must keep stdout JSON-clean per
-   * docs/progress-events.md) reports counts via its own PhaseResult instead.
-   * Errors/warnings still go to stderr regardless.
-   */
-  quiet?: boolean;
-  /**
-   * #3391: widen signature-drift invalidation to pages with NO recorded
-   * embedding_signature (pre-v108). By default those are grandfathered
-   * (never invalidated) so a routine upgrade doesn't surprise-re-embed a
-   * whole corpus — but after a provider/model swap the grandfather clause
-   * silently leaves them in the OLD embedding space, mixing two vector
-   * spaces in one index. `gbrain migrate embeddings` and
-   * `gbrain embed --stale --include-null-signature` set this.
-   */
-  includeNullSignature?: boolean;
 }
 
 /**
@@ -291,7 +253,7 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
     for (const s of opts.slugs) {
       if (isAborted(opts.signal)) break; // #1737: stop the per-slug loop on abort
       try {
-        await embedPage(engine, s, !!opts.dryRun, result, opts.sourceId, opts.signal, opts.quiet);
+        await embedPage(engine, s, !!opts.dryRun, result, opts.sourceId, opts.signal);
       } catch (e: unknown) {
         serr(`  Error embedding ${s}: ${e instanceof Error ? e.message : e}`);
       }
@@ -385,8 +347,6 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
         catchUp: opts.catchUp,
         pacer,
         paceMaxConcurrency,
-        quiet: opts.quiet,
-        includeNullSignature: opts.includeNullSignature,
       }, opts.signal);
     } finally {
       // E1: surface pacing telemetry (human + structured) when pacing was on.
@@ -416,7 +376,7 @@ export async function runEmbedCore(engine: BrainEngine, opts: EmbedOpts): Promis
     return result;
   }
   if (opts.slug) {
-    await embedPage(engine, opts.slug, !!opts.dryRun, result, opts.sourceId, opts.signal, opts.quiet);
+    await embedPage(engine, opts.slug, !!opts.dryRun, result, opts.sourceId, opts.signal);
     return result;
   }
   throw new Error('No embed target specified. Pass { slug }, { slugs }, { all }, or { stale }.');
@@ -500,8 +460,6 @@ export async function runEmbed(engine: BrainEngine, args: string[]): Promise<Emb
   const priorityRaw = priorityIdx >= 0 ? args[priorityIdx + 1] : undefined;
   const priority = priorityRaw === 'recent' ? 'recent' as const : undefined;
   const catchUp = args.includes('--catch-up');
-  // #3391: re-embed pages that predate the embedding_signature stamp too.
-  const includeNullSignature = args.includes('--include-null-signature');
   const pace = parsePaceArgs(args);
 
   let opts: EmbedOpts;
@@ -509,11 +467,11 @@ export async function runEmbed(engine: BrainEngine, args: string[]): Promise<Emb
     opts = { slugs: args.slice(slugsIdx + 1).filter(a => !a.startsWith('--')), dryRun, sourceId, batchSize, priority, catchUp };
   } else if (all || stale) {
     // E-2: CLI-only single-flight for stale runs (the minion path locks itself).
-    opts = { all, stale, dryRun, sourceId, batchSize, priority, catchUp, ...(pace && { pace }), ...(stale && { singleFlight: true }), ...(includeNullSignature && { includeNullSignature: true }) };
+    opts = { all, stale, dryRun, sourceId, batchSize, priority, catchUp, ...(pace && { pace }), ...(stale && { singleFlight: true }) };
   } else {
     const slug = args.find(a => !a.startsWith('--'));
     if (!slug) {
-      serr('Usage: gbrain embed [<slug>|--all|--stale|--slugs s1 s2 ...] [--dry-run] [--batch-size N] [--priority recent] [--catch-up] [--include-null-signature]');
+      serr('Usage: gbrain embed [<slug>|--all|--stale|--slugs s1 s2 ...] [--dry-run] [--batch-size N] [--priority recent] [--catch-up]');
       process.exit(1);
     }
     opts = { slug, dryRun, sourceId, batchSize, priority, catchUp };
@@ -563,7 +521,6 @@ async function embedPage(
   result: EmbedResult,
   sourceId?: string,
   signal?: AbortSignal,
-  quiet?: boolean,
 ) {
   const opts = sourceId ? { sourceId } : undefined;
   const page = await engine.getPage(slug, opts);
@@ -608,7 +565,7 @@ async function embedPage(
   result.skipped += chunks.length - toEmbed.length;
 
   if (toEmbed.length === 0) {
-    if (!quiet) slog(`${slug}: all ${chunks.length} chunks already embedded`);
+    slog(`${slug}: all ${chunks.length} chunks already embedded`);
     result.pages_processed++;
     return;
   }
@@ -619,16 +576,12 @@ async function embedPage(
     return;
   }
 
-  // #3507: embed with the page's STORED wrapping convention (title-tier
-  // contextual prefix when the page was embedded wrapped), not raw
-  // chunk_text — otherwise a re-embed silently strips the contextual
-  // prefixes the sync path applied. fenced_code chunks stay unwrapped.
-  const embeddings = await embedBatch(wrapChunkTextsForStoredMode(page, toEmbed), { abortSignal: signal });
+  const embeddings = await embedBatch(toEmbed.map(c => c.chunk_text), { abortSignal: signal });
   const embeddingMap = new Map<number, Float32Array>();
   for (let j = 0; j < toEmbed.length; j++) {
     embeddingMap.set(toEmbed[j].chunk_index, embeddings[j]);
   }
-  const updated: ChunkInput[] = chunks.map(c => preserveCodeMetadata(c, {
+  const updated: ChunkInput[] = chunks.map(c => ({
     chunk_index: c.chunk_index,
     chunk_text: c.chunk_text,
     chunk_source: c.chunk_source,
@@ -646,38 +599,10 @@ async function embedPage(
   // such a page and then stamps it.
   if (toEmbed.length === chunks.length) {
     await engine.setPageEmbeddingSignature(slug, { sourceId, signature: currentEmbeddingSignature() });
-    // #3507: a fully re-embedded per_chunk_synopsis page landed at the
-    // title tier — keep the stamped mode honest.
-    await restampIfDemotedToTitleTier(engine, page, slug, page.source_id);
   }
   result.embedded += toEmbed.length;
   result.pages_processed++;
-  if (!quiet) slog(`${slug}: embedded ${toEmbed.length} chunks`);
-}
-
-/**
- * Carry code-chunk metadata (language, symbol_name, symbol_type, line range,
- * parent scope, doc comment, qualified name) from a loaded Chunk back into a
- * ChunkInput destined for upsertChunks.
- *
- * Issue #769: every re-embed used to strip these fields, and upsertChunks
- * overwrites (does not COALESCE) the metadata columns from EXCLUDED, so
- * each pass clobbered code-def's primary index to NULL. Pulling the
- * preservation into one helper keeps the three re-embed call sites
- * (embedPage, embedAll non-stale, embedAllStale) in lock-step.
- */
-function preserveCodeMetadata(loaded: any, base: ChunkInput): ChunkInput {
-  return {
-    ...base,
-    language: loaded.language ?? undefined,
-    symbol_name: loaded.symbol_name ?? undefined,
-    symbol_type: loaded.symbol_type ?? undefined,
-    start_line: loaded.start_line ?? undefined,
-    end_line: loaded.end_line ?? undefined,
-    parent_symbol_path: loaded.parent_symbol_path ?? undefined,
-    doc_comment: loaded.doc_comment ?? undefined,
-    symbol_name_qualified: loaded.symbol_name_qualified ?? undefined,
-  };
+  slog(`${slug}: embedded ${toEmbed.length} chunks`);
 }
 
 async function embedAll(
@@ -695,10 +620,6 @@ async function embedAll(
     pacer?: DbPacer;
     /** Resolved concurrency cap (E-1: the worker count, no separate permit). */
     paceMaxConcurrency?: number;
-    /** #394: suppress human stdout summaries (structured-output callers). */
-    quiet?: boolean;
-    /** #3391: lift the NULL-signature grandfather clause (see EmbedOpts). */
-    includeNullSignature?: boolean;
   },
   signal?: AbortSignal,
 ) {
@@ -790,17 +711,14 @@ async function embedAll(
     }
 
     try {
-      // #3507: reproduce the page's stored wrapping convention (see embedPage).
-      const embeddings = await embedBatch(wrapChunkTextsForStoredMode(page, toEmbed));
+      const embeddings = await embedBatch(toEmbed.map(c => c.chunk_text));
       // Build a map of new embeddings by chunk_index
       const embeddingMap = new Map<number, Float32Array>();
       for (let j = 0; j < toEmbed.length; j++) {
         embeddingMap.set(toEmbed[j].chunk_index, embeddings[j]);
       }
-      // Preserve ALL chunks, only update embeddings for stale ones.
-      // preserveCodeMetadata threads code-chunk metadata (#769) so re-embed
-      // doesn't clobber language/symbol_name/symbol_type to NULL.
-      const updated: ChunkInput[] = chunks.map(c => preserveCodeMetadata(c, {
+      // Preserve ALL chunks, only update embeddings for stale ones
+      const updated: ChunkInput[] = chunks.map(c => ({
         chunk_index: c.chunk_index,
         chunk_text: c.chunk_text,
         chunk_source: c.chunk_source,
@@ -813,11 +731,6 @@ async function embedAll(
       await observed(pacer, () =>
         engine.setPageEmbeddingSignature(page.slug, { sourceId: pageSourceId, signature }),
       );
-      // #3507: --all fully re-embeds; a per_chunk_synopsis page landed at
-      // the title tier — keep the stamped mode honest.
-      await observed(pacer, () =>
-        restampIfDemotedToTitleTier(engine, page, page.slug, pageSourceId),
-      );
       result.embedded += toEmbed.length;
     } catch (e: unknown) {
       serr(`\n  Error embedding ${page.slug}: ${e instanceof Error ? e.message : e}`);
@@ -850,12 +763,10 @@ async function embedAll(
   });
 
   // Stdout summary preserved for scripts/tests that grep for counts.
-  if (!staleOpts?.quiet) {
-    if (dryRun) {
-      slog(`[dry-run] Would embed ${result.would_embed} chunks across ${pages.length} pages`);
-    } else {
-      slog(`Embedded ${result.embedded} chunks across ${pages.length} pages`);
-    }
+  if (dryRun) {
+    slog(`[dry-run] Would embed ${result.would_embed} chunks across ${pages.length} pages`);
+  } else {
+    slog(`Embedded ${result.embedded} chunks across ${pages.length} pages`);
   }
 }
 
@@ -891,10 +802,6 @@ async function embedAllStale(
     pacer?: DbPacer;
     /** Resolved concurrency cap (E-1: the worker count, no separate permit). */
     paceMaxConcurrency?: number;
-    /** #394: suppress human stdout summaries (structured-output callers). */
-    quiet?: boolean;
-    /** #3391: lift the NULL-signature grandfather clause (see EmbedOpts). */
-    includeNullSignature?: boolean;
   },
   signature?: string,
   externalSignal?: AbortSignal,
@@ -902,7 +809,6 @@ async function embedAllStale(
   // D7: thread sourceId so source-scoped runs only count + visit
   // that source's NULL embeddings.
   const sourceOpt = sourceId ? { sourceId } : undefined;
-  const includeNullSig = !!staleOpts?.includeNullSignature;
 
   // v0.41.31: re-embed pages whose embedding_signature drifted (model/dims
   // swap). dry-run must NOT mutate, so it counts signature-stale via the
@@ -912,54 +818,22 @@ async function embedAllStale(
     const invalidated = await engine.invalidateStaleSignatureEmbeddings({
       signature,
       ...(sourceId && { sourceId }),
-      ...(includeNullSig && { includeNullSignature: true }),
     });
-    if (invalidated > 0 && !staleOpts?.quiet) {
+    if (invalidated > 0) {
       slog(`[embed] invalidated ${invalidated} chunk(s) embedded under a prior model signature`);
     }
-    // #3391: the grandfather clause keeps NULL-signature pages on their OLD
-    // vectors — two embedding spaces mixed in one index. Loud stderr warning
-    // with the fix, instead of silent retrieval degradation.
-    //
-    // Deliberately NOT gated on `invalidated > 0`: the original bug report's
-    // shape is a brain where EVERY embedded page predates the signature stamp,
-    // so nothing drifts, nothing is invalidated — and pre-fix that brain got
-    // no warning AND no work, the exact silent case #3391 is about. The probe
-    // below computes the left-behind count directly, which is 0 on a healthy
-    // brain, so an unaffected run stays quiet.
-    if (!includeNullSig) {
-      try {
-        const wide = await engine.countStaleChunks({ ...sourceOpt, signature, includeNullSignature: true });
-        const narrow = await engine.countStaleChunks({ ...sourceOpt, signature });
-        const leftBehind = wide - narrow;
-        if (leftBehind > 0) {
-          serr(
-            `  [embed] WARNING: ${leftBehind} embedded chunk(s) sit on pages with no recorded ` +
-            `embedding signature and were NOT invalidated — they remain in the previous model's ` +
-            `embedding space. Re-run with --include-null-signature (or use ` +
-            `\`gbrain migrate embeddings\`) to re-embed them.`,
-          );
-        }
-      } catch {
-        // The warning probe is best-effort; never break the embed run.
-      }
-    }
   }
 
   // Pre-flight: 0 stale chunks → nothing to do, no further DB reads.
   // dry-run includes signature-drift in the count without mutating.
   const staleCount = await engine.countStaleChunks(
-    dryRun && signature
-      ? { ...sourceOpt, signature, ...(includeNullSig && { includeNullSignature: true }) }
-      : sourceOpt,
+    dryRun && signature ? { ...sourceOpt, signature } : sourceOpt,
   );
   if (staleCount === 0) {
-    if (!staleOpts?.quiet) {
-      if (dryRun) {
-        slog('[dry-run] Would embed 0 chunks (0 stale found)');
-      } else {
-        slog('Embedded 0 chunks (0 stale found)');
-      }
+    if (dryRun) {
+      slog('[dry-run] Would embed 0 chunks (0 stale found)');
+    } else {
+      slog('Embedded 0 chunks (0 stale found)');
     }
     return;
   }
@@ -968,7 +842,7 @@ async function embedAllStale(
     result.would_embed += staleCount;
     result.total_chunks += staleCount;
     if (onProgress) onProgress(1, 1, 0);
-    if (!staleOpts?.quiet) slog(`[dry-run] Would embed ${staleCount} stale chunks`);
+    slog(`[dry-run] Would embed ${staleCount} stale chunks`);
     return;
   }
 
@@ -1131,23 +1005,14 @@ async function embedAllStale(
         const keySourceId = stale[0]?.source_id ?? 'default';
         const slug = stale[0].slug;
         try {
-          // #3507: fetch the page row for its title + stored CR mode so the
-          // re-embed reproduces the page's wrapping convention instead of
-          // silently stripping contextual prefixes — `embed --stale` is the
-          // NORMAL post-model-migration path, so raw-text embedding here
-          // quietly converted whole corpora to the unwrapped convention.
-          const pageRow = await observed(pacer, () => engine.getPage(slug, { sourceId: keySourceId }));
-          const embeddings = await embedBatchWithBackoff(wrapChunkTextsForStoredMode(pageRow, stale), { abortSignal: effectiveSignal });
+          const embeddings = await embedBatchWithBackoff(stale.map(c => c.chunk_text), { abortSignal: effectiveSignal });
           // Re-fetch existing chunks and merge to avoid deleting non-stale chunks.
           const existing = await observed(pacer, () => engine.getChunks(slug, { sourceId: keySourceId }));
           const staleIdxToEmbedding = new Map<number, Float32Array>();
           for (let j = 0; j < stale.length; j++) {
             staleIdxToEmbedding.set(stale[j].chunk_index, embeddings[j]);
           }
-          // preserveCodeMetadata threads code-chunk metadata (#769) so the
-          // autopilot --stale path doesn't clobber language/symbol_name/etc
-          // to NULL on every cycle.
-          const merged: ChunkInput[] = existing.map(c => preserveCodeMetadata(c, {
+          const merged: ChunkInput[] = existing.map(c => ({
             chunk_index: c.chunk_index,
             chunk_text: c.chunk_text,
             chunk_source: c.chunk_source,
@@ -1165,14 +1030,6 @@ async function embedAllStale(
               engine.setPageEmbeddingSignature(slug, { sourceId: keySourceId, signature }),
             );
           }
-          // #3507: a FULLY re-embedded per_chunk_synopsis page landed at the
-          // title tier — keep the stamped mode honest. Partially-stale pages
-          // stay stamped as-is (mixed provenance; reindex sweeps fix them).
-          if (stale.length === existing.length) {
-            await observed(pacer, () =>
-              restampIfDemotedToTitleTier(engine, pageRow, slug, keySourceId),
-            );
-          }
           result.embedded += stale.length;
         } catch (e: unknown) {
           // Budget/abort-fired cancellations are expected on the way out; don't
@@ -1225,7 +1082,7 @@ async function embedAllStale(
     if (budgetTimer) clearTimeout(budgetTimer);
   }
 
-  if (!staleOpts?.quiet) slog(`Embedded ${result.embedded} chunks across ${totalProcessedPages} pages`);
+  slog(`Embedded ${result.embedded} chunks across ${totalProcessedPages} pages`);
 
   // #1946 (OV2a): a catch-up pass that completed without being aborted but left
   // chunks unembedded means those chunks are stuck (a non-transient embed
@@ -1233,9 +1090,7 @@ async function embedAllStale(
   // as a clean run — re-running won't help until the underlying failure is fixed.
   if (staleOpts?.catchUp && !effectiveSignal.aborted && embedFailures > 0) {
     const remaining = await engine.countStaleChunks(
-      signature
-        ? { signature, ...(sourceId ? { sourceId } : {}), ...(includeNullSig && { includeNullSignature: true }) }
-        : (sourceId ? { sourceId } : undefined),
+      signature ? { signature, ...(sourceId ? { sourceId } : {}) } : (sourceId ? { sourceId } : undefined),
     );
     if (remaining > 0) {
       serr(`\n  [embed] catch-up finished but ${remaining} chunk(s) remain stale after ${embedFailures} embed failure(s). These are not embeddable as-is; re-running won't clear them until the underlying error is resolved.`);

src/commands/eval-cross-modal.ts

@@ -76,7 +76,7 @@ FLAGS:
                            dimensions (goal, depth, sourcing, specificity, useful).
   --cycles N               1-3. Default: 3 in TTY, 1 in non-TTY (T11). Each
                            cycle is 3 model calls; verdict aggregates over them.
-  --slot-a-model <id>      Override default 'openai:gpt-5.2'.
+  --slot-a-model <id>      Override default 'openai:gpt-4o'.
   --slot-b-model <id>      Override default 'anthropic:claude-opus-4-7'.
   --slot-c-model <id>      Override default 'google:gemini-1.5-pro'.
   --receipt-dir <path>     Default: gbrainPath('eval-receipts').
@@ -468,14 +468,6 @@ interface BatchRow {
   question_id: string;
   question: string;
   hypothesis: string;
-  /**
-   * Gold answer from the benchmark dataset, when the upstream eval emits
-   * it (eval-longmemeval does). Folded into the judge task so CORRECTNESS
-   * is verifiable — without it a judge panel that sees only
-   * {question, hypothesis} cannot validate a terse factual answer against
-   * a haystack it never saw.
-   */
-  answer?: string;
 }
 
 /**
@@ -589,7 +581,6 @@ function readBatchRows(path: string): BatchReadResult {
       question_id: typeof obj.question_id === 'string' ? obj.question_id : `line-${lineNo}`,
       question: obj.question,
       hypothesis: obj.hypothesis,
-      ...(typeof obj.answer === 'string' && obj.answer.length > 0 ? { answer: obj.answer } : {}),
     });
   }
   if (summarySkipped > 0) {
@@ -706,11 +697,7 @@ async function runBatchMode(parsed: ParsedArgs, opts: RunCrossModalOpts): Promis
       fn: async (row, idx) => {
         process.stderr.write(`[eval cross-modal batch] ${idx + 1}/${rows.length} ${row.question_id} starting...\n`);
         return await runEvalFn({
-          // With a gold answer the judges can actually verify correctness;
-          // without one they see only {question, hypothesis} and cannot.
-          task: row.answer
-            ? `${row.question}\n\nExpected answer (gold label from the benchmark dataset): ${row.answer}`
-            : row.question,
+          task: row.question,
           output: row.hypothesis,
           slug: row.question_id,
           dimensions,

src/commands/eval-longmemeval.ts

@@ -33,7 +33,6 @@ import {
   type AliasMap,
 } from '../eval/longmemeval/extract.ts';
 import { extractCandidateEntities } from '../core/think/entity-extract.ts';
-import { splitProviderModelId } from '../core/model-id.ts';
 import { resolveEntitySlugWithSource, type ResolutionSource } from '../core/entities/resolve.ts';
 import { formatTrajectoryBlock } from '../core/trajectory-format.ts';
 
@@ -470,22 +469,14 @@ export async function runEvalLongMemEval(args: string[], runOpts: RunOpts = {}):
   });
 
   // Wrap Anthropic SDK so its `.messages.create` shape matches ThinkLLMClient.
-  // Same pattern as src/core/think/index.ts:247-249 — EXCEPT think's default
-  // client routes through the gateway, which parses `provider:model` recipe
-  // ids. This eval's client is a raw SDK by design (hermetic, no gateway
-  // dependency), and resolveModel returns RECIPE ids (`anthropic:claude-…`);
-  // passing one through unstripped 404s every answer/extractor call, which
-  // surfaces downstream as all-upstream_error batches in the nightly probe.
-  const toSdkModel = (m: string): string => splitProviderModelId(m).model || m;
+  // Same pattern as src/core/think/index.ts:247-249.
   const realClient = new Anthropic();
   const client: ThinkLLMClient = runOpts.client ?? {
-    create: (params, callOpts) =>
-      realClient.messages.create({ ...params, model: toSdkModel(params.model) }, callOpts),
+    create: (params, callOpts) => realClient.messages.create(params, callOpts),
   };
   // v0.40.2.0 — separate extractor client (defaults to same SDK).
   const extractorClient: ThinkLLMClient = runOpts.extractorClient ?? {
-    create: (params, callOpts) =>
-      realClient.messages.create({ ...params, model: toSdkModel(params.model) }, callOpts),
+    create: (params, callOpts) => realClient.messages.create(params, callOpts),
   };
   const trajectoryEnabled = !opts.noTrajectory;
   const extractorModel = trajectoryEnabled
@@ -760,11 +751,6 @@ async function runOneQuestion(
     // v0.40.1.0 (Track D / T2) — copy question_type into the row so the
     // by_type_summary can be rebuilt from the file on resume runs.
     question_type: q.question_type,
-    // Gold answer for downstream consumers that verify correctness (the
-    // cross-modal --batch judge folds it into the task; evaluate_qa.py
-    // ignores unknown fields). Without it a judge can't validate a terse
-    // factual hypothesis against a haystack it never saw.
-    ...(q.answer !== undefined ? { answer: q.answer } : {}),
     hypothesis,
     retrieved_session_ids: retrievedSessionIds,
     ...(recallHit !== undefined ? { recall_hit: recallHit } : {}),

src/commands/extract-conversation-facts.ts

@@ -43,10 +43,11 @@
  *     (source_id, source_markdown_slug, row_num); per-segment row_num
  *     would collide on segment 2. Per-page counter increments across
  *     segments.
- *   - Snapshot-bound terminal audit row on completion. After all segments
- *     commit, one v2 row binds completion to the exact page version or raw
- *     transcript digest. Partial extraction has no matching terminal and the
- *     next claim performs a delete-first full replay.
+ *   - Terminal audit row on completion. After all segments commit, one
+ *     extra fact row with source='cli:extract-conversation-facts:terminal'
+ *     marks the page complete. Doctor's backlog query checks for the
+ *     terminal row, NOT any fact — partial extraction → no terminal →
+ *     next run resumes.
  *   - Optional budgetTracker via opts. If a tracker is in opts, use it
  *     as-is (NO `withBudgetTracker` wrap, which would REPLACE the active
  *     tracker per gateway.ts AsyncLocalStorage semantics, defeating an
@@ -67,7 +68,7 @@
 import type { BrainEngine, NewFact } from '../core/engine.ts';
 import type { Page } from '../core/types.ts';
 import {
-  extractFactsFromTurnWithOutcome,
+  extractFactsFromTurn,
   isFactsExtractionEnabled,
 } from '../core/facts/extract.ts';
 import { configureGatewayIfUninitialized, isAvailable, withBudgetTracker } from '../core/ai/gateway.ts';
@@ -149,40 +150,6 @@ export const ALLOWED_TYPES = [
 ] as const;
 export type AllowedType = (typeof ALLOWED_TYPES)[number];
 
-/**
- * Granular collector page-types that alias into each canonical conversation
- * bucket. The v2 type-consolidation pack retypes these to the canonical names
- * (`slack-dm-day`/`slack-thread` → `slack`, `email-digest` → `email`), but a
- * brain that hasn't run that pack still carries the collector's granular types
- * in `pages.type`. Without this expansion, `listPages({ type: 'slack' })`
- * matches zero rows on such brains and the whole comms corpus is silently
- * skipped (facts stay empty → `find_trajectory` returns nothing). The canonical
- * name is always included first so consolidated brains keep working unchanged.
- */
-export const ALLOWED_TYPE_ALIASES: Record<AllowedType, readonly string[]> = {
-  conversation: ['conversation'],
-  meeting: ['meeting'],
-  slack: ['slack', 'slack-dm-day', 'slack-thread'],
-  email: ['email', 'email-digest'],
-  imessage: ['imessage'],
-  'imessage-daily': ['imessage-daily'],
-};
-
-/**
- * Expand the requested logical types to the concrete `pages.type` values to
- * enumerate, canonical-first and de-duplicated. Unknown types pass through
- * unchanged so an explicit override is never dropped.
- */
-export function pageTypesForAllowed(types: readonly AllowedType[]): string[] {
-  const out: string[] = [];
-  for (const t of types) {
-    for (const concrete of ALLOWED_TYPE_ALIASES[t] ?? [t]) {
-      if (!out.includes(concrete)) out.push(concrete);
-    }
-  }
-  return out;
-}
-
 /**
  * Pagination batch size for listPages enumeration. Per-batch memory
  * worst case = BATCH × MAX_PAGE_BODY_BYTES = 250MB at default 10
@@ -205,15 +172,7 @@ export const PER_SEGMENT_SOURCE_PREFIX = 'cli:extract-conversation-facts';
  * the per-segment source. Partial extraction = no terminal row = page
  * stays in backlog.
  */
-export const TERMINAL_AUDIT_SOURCE = 'cli:extract-conversation-facts:terminal:v2';
-
-/**
- * Durable outcome for a successfully scanned page that contains no eligible
- * multi-message segment. Kept distinct from successful extraction so operator
- * surfaces can report the truth without rescanning the page forever.
- */
-export const NON_EXTRACTABLE_AUDIT_SOURCE =
-  'cli:extract-conversation-facts:non-extractable:v2';
+export const TERMINAL_AUDIT_SOURCE = 'cli:extract-conversation-facts:terminal';
 
 // ---------------------------------------------------------------------------
 // Public types.
@@ -294,19 +253,6 @@ export interface ExtractConversationFactsResult {
   pages_skipped: number;
   pages_skipped_too_large: number;
   pages_skipped_disappeared: number;
-  /** Fresh terminal outcomes skipped before parsing or model work. */
-  pages_skipped_completed: number;
-  /** Fresh scanned-not-extractable outcomes skipped before parser work. */
-  pages_skipped_non_extractable: number;
-  /** Durable scanned-not-extractable outcomes written by this run. */
-  pages_marked_non_extractable: number;
-  /** Pages whose claim reached extraction but failed before durable outcome. */
-  pages_failed: number;
-  /**
-   * Pages whose built-in parse returned `no_match` and whose messages were
-   * recovered by the explicitly enabled LLM fallback.
-   */
-  pages_llm_fallback: number;
   /**
    * v0.41.15.0 (D6): pages we attempted to claim but skipped because
    * another worker / parallel process held the advisory lock. The pages
@@ -344,13 +290,10 @@ export interface ExtractConversationFactsResult {
 // ---------------------------------------------------------------------------
 
 import {
-  deriveDateContext,
   parseConversation,
   type ParseConversationOpts as OrchestratorParseOpts,
 } from '../core/conversation-parser/parse.ts';
 import { readConversationBodyForParsing } from '../core/conversation-parser/body.ts';
-import { runLlmFallback } from '../core/conversation-parser/llm-fallback.ts';
-import { resolveModel } from '../core/model-config.ts';
 
 /**
  * v0.41.13.0 — back-compat shape for direct callers + the existing
@@ -640,21 +583,31 @@ async function deleteOrphanFactsForPage(
   sourceId: string,
   slug: string,
 ): Promise<number> {
-  // A cleanup failure is authoritative: callers must not write a terminal or
-  // non-extractable marker while facts from an older snapshot may remain.
-  const rows = await engine.executeRaw<{ count: string }>(
-    `WITH del AS (
-       DELETE FROM facts
-       WHERE source_id = $1
-         AND source_markdown_slug = $2
-         AND source LIKE 'cli:extract-conversation-facts%'
-       RETURNING 1
-     )
-     SELECT COUNT(*)::text AS count FROM del`,
-    [sourceId, slug],
-  );
-  const n = parseInt(rows[0]?.count ?? '0', 10);
-  return Number.isFinite(n) ? n : 0;
+  try {
+    // The two write-source variants this command may have left behind:
+    //   - PER_SEGMENT_SOURCE_PREFIX  ('cli:extract-conversation-facts')
+    //   - TERMINAL_AUDIT_SOURCE      ('cli:extract-conversation-facts:terminal')
+    // Using a LIKE prefix match covers both with one statement.
+    const rows = await engine.executeRaw<{ count: string }>(
+      `WITH del AS (
+         DELETE FROM facts
+         WHERE source_id = $1
+           AND source_markdown_slug = $2
+           AND source LIKE 'cli:extract-conversation-facts%'
+         RETURNING 1
+       )
+       SELECT COUNT(*)::text AS count FROM del`,
+      [sourceId, slug],
+    );
+    const n = parseInt(rows[0]?.count ?? '0', 10);
+    return Number.isFinite(n) ? n : 0;
+  } catch {
+    // Best-effort: a missing source_markdown_slug column on pre-v0.32
+    // brains (or other rare DDL drift) falls through to "no orphans
+    // cleaned." The subsequent insertFacts call will surface any real
+    // schema issues with a clearer error.
+    return 0;
+  }
 }
 
 // ---------------------------------------------------------------------------
@@ -678,12 +631,6 @@ interface ExtractCoreState {
    * batch boundaries + final flush.
    */
   cpMap: Map<string, string>;
-  /**
-   * Opt-in LLM parser state, resolved once per source run. A null model means
-   * the fallback is disabled and no chat content leaves the deterministic
-   * parser path.
-   */
-  llmFallbackModel: string | null;
 }
 
 function cpMapKey(sourceId: string, slug: string): string {
@@ -716,150 +663,11 @@ function cpEntriesToMap(entries: string[]): Map<string, string> {
   return map;
 }
 
-export type DurableExtractionOutcome = 'complete' | 'non_extractable';
-
-interface ConversationPageSnapshot {
-  page: Page;
-  body: string;
-  versionToken: string;
-}
-
-function hasRawTranscriptSidecar(page: Page): boolean {
-  const raw = page.frontmatter?.raw_transcript;
-  return typeof raw === 'string' && raw.trim().length > 0;
-}
-
-function regularPageVersionToken(page: Page): string {
-  // content_hash covers title, type, compiled_truth, timeline, and frontmatter.
-  // Unlike JavaScript Date, it cannot collapse distinct PostgreSQL updates that
-  // happen within the same millisecond. effective_date is parser input too.
-  const hash = page.content_hash ?? createHash('sha256')
-    .update(JSON.stringify({
-      title: page.title,
-      type: page.type,
-      compiled_truth: page.compiled_truth,
-      timeline: page.timeline || '',
-      frontmatter: page.frontmatter || {},
-    }))
-    .digest('hex');
-  const effectiveDate = page.effective_date
-    ? new Date(page.effective_date).toISOString().slice(0, 10)
-    : 'none';
-  return `page-${hash}-${effectiveDate}`;
-}
-
-function snapshotVersionToken(page: Page, body: string): string {
-  if (!hasRawTranscriptSidecar(page)) return regularPageVersionToken(page);
-  // Sidecar contents can change without touching pages.updated_at. Hash the
-  // exact parser input plus parser-relevant page metadata so those edits reopen
-  // the page without a schema migration.
-  return `sidecar-${createHash('sha256')
-    .update(
-      JSON.stringify({
-        body,
-        title: page.title,
-        type: page.type,
-        frontmatter: page.frontmatter,
-        effective_date: page.effective_date ?? null,
-      }),
-    )
-    .digest('hex')}`;
-}
-
-async function preparePageSnapshot(
-  engine: BrainEngine,
-  page: Page,
-): Promise<ConversationPageSnapshot> {
-  const body = await readConversationBodyForParsing(engine, page);
-  return { page, body, versionToken: snapshotVersionToken(page, body) };
-}
-
-function outcomeSession(source: string, slug: string, versionToken: string): string {
-  return `${source}:${slug}:${versionToken}`;
-}
-
-/**
- * Find v2 outcomes bound to the exact parser input snapshot. Legacy outcome
- * rows deliberately do not match and are replayed once under the strict v2
- * protocol. Sidecar files are hashed because pages.updated_at cannot see them.
- */
-export async function findFreshExtractionOutcomes(
-  engine: BrainEngine,
-  sourceId: string,
-  pages: readonly Page[],
-): Promise<Map<string, DurableExtractionOutcome>> {
-  if (pages.length === 0) return new Map();
-  const expected = new Map<string, string>();
-  for (const page of pages) {
-    // Batch enumeration can already be stale. Refresh before deciding to skip
-    // so an edit between listPages and this check cannot match an old marker.
-    const current = await engine.getPage(page.slug, { sourceId });
-    if (!current) continue;
-    const token = hasRawTranscriptSidecar(current)
-      ? (await preparePageSnapshot(engine, current)).versionToken
-      : regularPageVersionToken(current);
-    expected.set(current.slug, token);
-  }
-  const rows = await engine.executeRaw<{
-    slug: string;
-    source: string;
-    source_session: string | null;
-  }>(
-    `SELECT source_markdown_slug AS slug, source, source_session
-       FROM facts
-      WHERE source_id = $1
-        AND source_markdown_slug = ANY($2::text[])
-        AND source = ANY($3::text[])
-      ORDER BY source_markdown_slug,
-        CASE WHEN source = $4 THEN 0 ELSE 1 END`,
-    [
-      sourceId,
-      pages.map((page) => page.slug),
-      [TERMINAL_AUDIT_SOURCE, NON_EXTRACTABLE_AUDIT_SOURCE],
-      TERMINAL_AUDIT_SOURCE,
-    ],
-  );
-  const outcomes = new Map<string, DurableExtractionOutcome>();
-  for (const row of rows) {
-    if (outcomes.has(row.slug)) continue;
-    const token = expected.get(row.slug);
-    if (!token || row.source_session !== outcomeSession(row.source, row.slug, token)) {
-      continue;
-    }
-    outcomes.set(
-      row.slug,
-      row.source === TERMINAL_AUDIT_SOURCE ? 'complete' : 'non_extractable',
-    );
-  }
-  return outcomes;
-}
-
-function recordDurableOutcomeSkip(
-  state: ExtractCoreState,
-  outcome: DurableExtractionOutcome,
-): void {
-  state.result.pages_considered++;
-  if (outcome === 'complete') state.result.pages_skipped_completed++;
-  else state.result.pages_skipped_non_extractable++;
-}
-
-async function snapshotIsCurrent(
-  engine: BrainEngine,
-  sourceId: string,
-  snapshot: ConversationPageSnapshot,
-): Promise<boolean> {
-  const current = await engine.getPage(snapshot.page.slug, { sourceId });
-  if (!current) return false;
-  const currentSnapshot = await preparePageSnapshot(engine, current);
-  return currentSnapshot.versionToken === snapshot.versionToken;
-}
-
 async function processPage(
   state: ExtractCoreState,
-  snapshot: ConversationPageSnapshot,
+  page: Page,
   sinceIso: string | undefined,
 ): Promise<{ newEndIso: string | null }> {
-  const { page, body } = snapshot;
   state.result.pages_considered++;
 
   // Body cap check first — pre-parse, pre-segment, pre-extraction.
@@ -872,6 +680,7 @@ async function processPage(
     return { newEndIso: null };
   }
 
+  const body = await readConversationBodyForParsing(state.engine, page);
   // v0.41.13.0: thread the full Page through the orchestrator so D8
   // date-derivation chain (frontmatter.date > effective_date >
   // '1970-01-01') AND timezone_policy warnings apply. The historical
@@ -879,71 +688,13 @@ async function processPage(
   // meant Telegram-bracket pages with frontmatter dates landed at
   // 1970-01-01. Now they pick up the correct date.
   const parseResult = parseConversation(body, { page });
-  let messages = parseResult.messages;
+  const messages = parseResult.messages;
   if (parseResult.timezone_warning) {
     process.stderr.write(parseResult.timezone_warning + '\n');
   }
-  // The fallback runs only for a true built-in miss. It never replaces or
-  // polishes a deterministic parse, and it remains unreachable unless the
-  // operator explicitly enables conversation_parser.llm_fallback_enabled.
-  if (
-    !state.dryRun &&
-    messages.length === 0 &&
-    parseResult.phase === 'no_match' &&
-    state.llmFallbackModel
-  ) {
-    const fallbackMessages = await runLlmFallback({
-      modelStr: state.llmFallbackModel,
-      body,
-      engine: state.engine,
-      signal: state.signal,
-      fallbackDate: deriveDateContext({ page }).fallbackDate,
-      propagateError: (error) =>
-        error instanceof BudgetExhausted ||
-        (state.signal?.aborted === true && isAbortError(error)),
-    });
-    if (fallbackMessages && fallbackMessages.length > 0) {
-      messages = fallbackMessages;
-      state.result.pages_llm_fallback++;
-      process.stderr.write(
-        `[extract-conversation-facts] LLM fallback parsed ${fallbackMessages.length} message(s) for ${page.slug}\n`,
-      );
-    }
-  }
-  const allSegments = splitIntoSegments(messages);
   const segments = splitIntoSegments(messages, { sinceIso });
   if (segments.length === 0) {
     state.result.pages_skipped++;
-    if (
-      !state.dryRun &&
-      parseResult.phase !== 'no_match' &&
-      allSegments.length === 0
-    ) {
-      if (await snapshotIsCurrent(state.engine, state.sourceId, snapshot)) {
-        const cleaned = await deleteOrphanFactsForPage(
-          state.engine,
-          state.sourceId,
-          page.slug,
-        );
-        state.result.orphan_facts_cleaned += cleaned;
-        const rowNum = await peekRowNumStart(
-          state.engine,
-          state.sourceId,
-          page.slug,
-        );
-        await writeNonExtractableAuditRow(
-          state.engine,
-          state.sourceId,
-          page.slug,
-          rowNum,
-          snapshot.versionToken,
-          messages.length === 0
-            ? 'no conversation messages found'
-            : 'fewer than two eligible messages',
-        );
-        state.result.pages_marked_non_extractable++;
-      }
-    }
     return { newEndIso: null };
   }
 
@@ -979,22 +730,24 @@ async function processPage(
     const text = renderSegmentForExtraction(page.title || page.slug, seg);
     const sessionId = `${PER_SEGMENT_SOURCE_PREFIX}:${page.slug}`;
 
-    const extraction = await extractFactsFromTurnWithOutcome({
-      turnText: text,
-      sessionId,
-      source: PER_SEGMENT_SOURCE_PREFIX,
-      engine: state.engine,
-      abortSignal: state.signal,
-    });
-    if (!extraction.ok) {
-      const detail = extraction.error instanceof Error
-        ? `: ${extraction.error.message}`
-        : '';
-      throw new Error(
-        `segment ${seg.startIso}..${seg.endIso} extraction failed (${extraction.reason})${detail}`,
+    let extracted: Awaited<ReturnType<typeof extractFactsFromTurn>> = [];
+    try {
+      extracted = await extractFactsFromTurn({
+        turnText: text,
+        sessionId,
+        source: PER_SEGMENT_SOURCE_PREFIX,
+        engine: state.engine,
+        abortSignal: state.signal,
+      });
+    } catch (err) {
+      if (isAbortError(err)) throw err;
+      if (err instanceof BudgetExhausted) throw err;
+      // Per-segment LLM failures are best-effort; loop continues.
+      process.stderr.write(
+        `[extract-conversation-facts] segment ${seg.startIso}..${seg.endIso} extractor failed: ${(err as Error).message}\n`,
       );
+      extracted = [];
     }
-    const extracted = extraction.facts;
 
     state.result.segments_processed++;
     segmentsThisPage++;
@@ -1019,9 +772,19 @@ async function processPage(
         context:
           fact.context ?? `from ${page.slug} segment ${seg.startIso}..${seg.endIso}`,
       }));
-      const ins = await state.engine.insertFacts(rows, { source_id: state.sourceId }); // gbrain-allow-direct-insert: canonical bulk extraction path for conversation pages — fences-as-system-of-record doesn't apply because conversations don't carry `## Facts` fences (the chat-log shape is the source-of-truth)
-      pageInsertedTotal += ins.inserted;
-      state.result.facts_inserted += ins.inserted;
+      try {
+        const ins = await state.engine.insertFacts(rows, { source_id: state.sourceId }); // gbrain-allow-direct-insert: canonical bulk extraction path for conversation pages — fences-as-system-of-record doesn't apply because conversations don't carry `## Facts` fences (the chat-log shape is the source-of-truth)
+        pageInsertedTotal += ins.inserted;
+        state.result.facts_inserted += ins.inserted;
+      } catch (err) {
+        if (isAbortError(err)) throw err;
+        // Batch failure is best-effort — segment is the transactional
+        // boundary, so a duplicate-key or constraint error rolls back
+        // this segment only. Loop continues.
+        process.stderr.write(
+          `[extract-conversation-facts] segment ${seg.startIso}..${seg.endIso} insertFacts failed: ${(err as Error).message}\n`,
+        );
+      }
       rowNum += extracted.length;
     } else {
       // dry-run: count for reporting, no DB write.
@@ -1037,28 +800,20 @@ async function processPage(
   // segment (no break on segmentLimit; that's an explicit partial run).
   const fullyProcessed =
     state.segmentLimit === 0 || segmentsThisPage < state.segmentLimit;
-  if (
-    !state.dryRun &&
-    fullyProcessed &&
-    newestEnd !== null &&
-    await snapshotIsCurrent(state.engine, state.sourceId, snapshot)
-  ) {
-    // A terminal insert is part of the page transaction contract. Propagate
-    // failure so bulk accounting, CLI exit status, cycle status, and rollups all
-    // report the page as unfinished.
-    await writeTerminalAuditRow(
-      state.engine,
-      state.sourceId,
-      page.slug,
-      rowNum,
-      snapshot.versionToken,
-    );
-    rowNum++;
-  } else if (!state.dryRun && fullyProcessed && newestEnd !== null) {
-    process.stderr.write(
-      `[extract-conversation-facts] ${page.slug} changed during extraction; leaving it unfinished for replay\n`,
-    );
-    newestEnd = null;
+  if (!state.dryRun && fullyProcessed && newestEnd !== null) {
+    try {
+      await writeTerminalAuditRow(state.engine, state.sourceId, page.slug, rowNum);
+      rowNum++;
+    } catch (err) {
+      if (isAbortError(err)) throw err;
+      // Terminal-row write failure: page is NOT marked complete; next
+      // run resumes. Loud stderr so users see partial-success state.
+      process.stderr.write(
+        `[extract-conversation-facts] ${page.slug} terminal audit write failed: ${(err as Error).message}\n`,
+      );
+      // Suppress the resume-state update so doctor still flags this page.
+      newestEnd = null;
+    }
   }
 
   if (!state.dryRun && newestEnd !== null) {
@@ -1083,14 +838,13 @@ async function writeTerminalAuditRow(
   sourceId: string,
   slug: string,
   rowNum: number,
-  versionToken: string,
 ): Promise<void> {
   const fact: NewFact & { row_num: number; source_markdown_slug: string } = {
     fact: 'EXTRACTION_COMPLETE',
     kind: 'fact',
     entity_slug: null,
     source: TERMINAL_AUDIT_SOURCE,
-    source_session: outcomeSession(TERMINAL_AUDIT_SOURCE, slug, versionToken),
+    source_session: `${TERMINAL_AUDIT_SOURCE}:${slug}`,
     confidence: 1.0,
     notability: 'low',
     row_num: rowNum,
@@ -1109,33 +863,6 @@ async function writeTerminalAuditRow(
  *   - If absent: create a fresh tracker scoped to `opts.maxCostUsd`
  *     and run the body inside `withBudgetTracker`.
  */
-async function writeNonExtractableAuditRow(
-  engine: BrainEngine,
-  sourceId: string,
-  slug: string,
-  rowNum: number,
-  versionToken: string,
-  reason: string,
-): Promise<void> {
-  const fact: NewFact & { row_num: number; source_markdown_slug: string } = {
-    fact: 'EXTRACTION_NOT_APPLICABLE',
-    kind: 'fact',
-    entity_slug: null,
-    source: NON_EXTRACTABLE_AUDIT_SOURCE,
-    source_session: outcomeSession(
-      NON_EXTRACTABLE_AUDIT_SOURCE,
-      slug,
-      versionToken,
-    ),
-    confidence: 1.0,
-    notability: 'low',
-    context: `scanned, not extractable: ${reason}`,
-    row_num: rowNum,
-    source_markdown_slug: slug,
-  };
-  await engine.insertFacts([fact], { source_id: sourceId }); // gbrain-allow-direct-insert: durable non-extractable audit outcome prevents repeated scans while remaining distinct from successful extraction
-}
-
 export async function runExtractConversationFactsCore(
   engine: BrainEngine,
   opts: ExtractConversationFactsCoreOpts,
@@ -1152,11 +879,6 @@ export async function runExtractConversationFactsCore(
     pages_skipped: 0,
     pages_skipped_too_large: 0,
     pages_skipped_disappeared: 0,
-    pages_skipped_completed: 0,
-    pages_skipped_non_extractable: 0,
-    pages_marked_non_extractable: 0,
-    pages_failed: 0,
-    pages_llm_fallback: 0,
     pages_lock_skipped: 0,
     orphan_facts_cleaned: 0,
     segments_processed: 0,
@@ -1202,18 +924,6 @@ export async function runExtractConversationFactsCore(
   );
   const workers = workersResolved.workers;
 
-  // Privacy boundary: the parser never sends page content to an LLM unless
-  // this exact DB-plane key is explicitly true. Resolve the model once rather
-  // than probing configuration for every page.
-  const llmFallbackEnabled =
-    (await engine.getConfig('conversation_parser.llm_fallback_enabled')) === 'true';
-  const llmFallbackModel = llmFallbackEnabled
-    ? await resolveModel(engine, {
-        tier: 'utility',
-        fallback: 'anthropic:claude-haiku-4-5-20251001',
-      })
-    : null;
-
   const state: ExtractCoreState = {
     result,
     engine,
@@ -1224,7 +934,6 @@ export async function runExtractConversationFactsCore(
     types,
     signal,
     cpMap: new Map(),
-    llmFallbackModel,
   };
 
   // Run body. Either inside the externally-provided tracker scope (no
@@ -1248,41 +957,21 @@ export async function runExtractConversationFactsCore(
      */
     const processPageWithLock = async (page: Page): Promise<void> => {
       const lockId = extractConversationFactsLockId(sourceId, page.slug);
+
+      let sinceIso: string | undefined;
+      // Per-page resume: --force clears prior entries; normal path uses
+      // the latest endIso for this (sourceId, slug) from the shared map.
       if (opts.force) {
         state.cpMap.delete(cpMapKey(sourceId, page.slug));
       }
+      const checkpointed = state.cpMap.get(cpMapKey(sourceId, page.slug)) ?? null;
+      sinceIso = pickLaterIso(checkpointed, opts.sinceIso);
 
       try {
         await withRefreshingLock(
           engine,
           lockId,
-          async () => {
-            // Re-fetch under the advisory lock. Batch enumeration is only a
-            // candidate list; it must never become the snapshot we certify.
-            const currentPage = await engine.getPage(page.slug, { sourceId });
-            if (!currentPage) {
-              state.result.pages_skipped_disappeared++;
-              return { newEndIso: null };
-            }
-
-            // Close the race between batch selection and lock acquisition.
-            if (!opts.force) {
-              const outcome = (
-                await findFreshExtractionOutcomes(engine, sourceId, [currentPage])
-              ).get(currentPage.slug);
-              if (outcome) {
-                recordDurableOutcomeSkip(state, outcome);
-                return { newEndIso: null };
-              }
-            }
-
-            // A checkpoint without a matching durable v2 outcome cannot prove
-            // which page snapshot it describes. Clear it and replay safely;
-            // delete-orphans-first makes that replay deterministic.
-            state.cpMap.delete(cpMapKey(sourceId, currentPage.slug));
-            const snapshot = await preparePageSnapshot(engine, currentPage);
-            return processPage(state, snapshot, opts.sinceIso);
-          },
+          () => processPage(state, page, sinceIso),
           { ttlMinutes: PER_PAGE_LOCK_TTL_MINUTES },
         ).then(() => undefined);
       } catch (err) {
@@ -1298,18 +987,13 @@ export async function runExtractConversationFactsCore(
       }
     };
 
-    // Expand logical types (conversation/meeting/slack/email) to the concrete
-    // `pages.type` values to enumerate, so brains on the granular collector
-    // types are not silently skipped (see ALLOWED_TYPE_ALIASES).
-    const concreteTypes = pageTypesForAllowed(types);
-
     if (opts.slug) {
       const page = await engine.getPage(opts.slug, { sourceId });
       if (!page) {
         result.pages_skipped_disappeared++;
         return;
       }
-      if (!concreteTypes.includes(page.type)) {
+      if (!types.includes(page.type as AllowedType)) {
         result.pages_skipped++;
         return;
       }
@@ -1323,7 +1007,7 @@ export async function runExtractConversationFactsCore(
       // honors AbortSignal at each claim boundary and threads
       // BudgetExhausted abort (D13) automatically.
       let processedPagesCount = 0;
-      pageLoop: for (const type of concreteTypes) {
+      pageLoop: for (const type of types) {
         let offset = 0;
         // eslint-disable-next-line no-constant-condition
         while (true) {
@@ -1338,59 +1022,21 @@ export async function runExtractConversationFactsCore(
           });
           if (batch.length === 0) break;
 
+          // Respect --limit at batch granularity: clip the batch so we
+          // never overshoot the cap by `workers - 1` extra pages.
           let claimable = batch;
-          // Checkpoints are an intra-page cursor; fresh durable outcomes are
-          // the page-level selection authority and survive checkpoint GC.
-          if (!opts.force && claimable.length > 0) {
-            const fresh = await findFreshExtractionOutcomes(
-              engine,
-              sourceId,
-              claimable,
-            );
-            claimable = claimable.filter((page) => {
-              const outcome = fresh.get(page.slug);
-              if (!outcome) return true;
-              recordDurableOutcomeSkip(state, outcome);
-              return false;
-            });
-          }
-
-          // Apply --limit after durable filtering. The limit caps pages that
-          // need work, not already-completed pages scanned to find that work.
           if (opts.limit) {
             const remaining = opts.limit - processedPagesCount;
-            if (remaining < claimable.length) {
-              claimable = claimable.slice(0, remaining);
-            }
+            if (remaining < batch.length) claimable = batch.slice(0, remaining);
           }
 
-          const poolResult = await runSlidingPool({
+          await runSlidingPool({
             items: claimable,
             workers,
             signal,
             onItem: (page) => processPageWithLock(page),
-            onError: (error) => (isAbortError(error) ? 'abort' : 'continue'),
             failureLabel: (page) => page.slug,
           });
-          const cancellation = poolResult.failures.find((failure) =>
-            isAbortError(failure.error),
-          );
-          if (cancellation) throw cancellation.error;
-          if (signal?.aborted) {
-            if (signal.reason instanceof Error) throw signal.reason;
-            throw Object.assign(new Error('caller cancelled'), {
-              name: 'AbortError',
-            });
-          }
-          result.pages_failed += poolResult.errored;
-          for (const failure of poolResult.failures) {
-            const message = failure.error instanceof Error
-              ? failure.error.message
-              : String(failure.error);
-            process.stderr.write(
-              `[extract-conversation-facts] ${failure.label} failed: ${message}\n`,
-            );
-          }
 
           processedPagesCount += claimable.length;
           offset += batch.length;
@@ -1411,7 +1057,6 @@ export async function runExtractConversationFactsCore(
     }
   };
 
-  let ownedTracker: BudgetTracker | null = null;
   try {
     if (opts.budgetTracker) {
       // Caller-managed scope — use as-is, no wrap (nested wrap REPLACES
@@ -1422,7 +1067,6 @@ export async function runExtractConversationFactsCore(
         maxCostUsd: opts.maxCostUsd ?? DEFAULT_MAX_COST_USD,
         label: `extract-conversation-facts:${sourceId}`,
       });
-      ownedTracker = tracker;
       try {
         await withBudgetTracker(tracker, body);
       } finally {
@@ -1446,34 +1090,13 @@ export async function runExtractConversationFactsCore(
     throw err;
   }
 
-  // gateway.chat preserves a successful provider result when the final
-  // tracker.record() discovers an underestimated overage. Usually the next
-  // reserve surfaces it, but a fallback that yields fewer than two messages
-  // has no next call. Detect that terminal overage so the result and rollup
-  // remain honest.
-  const effectiveTracker = opts.budgetTracker ?? ownedTracker;
-  if (
-    effectiveTracker?.cap !== undefined &&
-    effectiveTracker.totalSpent > effectiveTracker.cap
-  ) {
-    result.budget_exhausted = true;
-    result.spent_usd = effectiveTracker.totalSpent;
-  }
-
   // v0.42 — Wave B1: extract-conversation-facts writes a receipt page
   // (queryable + citable per D-EXTRACT-17/19) AND UPSERTs the per-day
   // rollup row (best-effort cache per F-OUT-19). Both are best-effort —
   // failures stderr-warn but never fail the parent operation.
   // --dry-run must not persist cache/knowledge state: skip the rollup UPSERT +
   // receipt-page write so a preview leaves no extract cache row behind.
-  if (!dryRun) {
-    await writeRunReceiptAndRollup(
-      engine,
-      sourceId,
-      result,
-      /* halted */ result.budget_exhausted === true,
-    );
-  }
+  if (!dryRun) await writeRunReceiptAndRollup(engine, sourceId, result, /* halted */ false);
 
   return result;
 }
@@ -1511,12 +1134,7 @@ async function writeRunReceiptAndRollup(
         extracted_at: now,
         total_rows: result.facts_inserted,
         cost_usd: result.spent_usd ?? 0,
-        summary:
-          `Extracted ${result.facts_inserted} facts from ` +
-          `${result.pages_processed}/${result.pages_considered} eligible pages` +
-          (result.pages_failed > 0
-            ? `; ${result.pages_failed} page(s) failed and remain unfinished.`
-            : '.'),
+        summary: `Extracted ${result.facts_inserted} facts from ${result.pages_processed}/${result.pages_considered} eligible pages.`,
       });
     } catch (err) {
       // Best-effort: receipt write failure shouldn't kill the run.
@@ -1530,13 +1148,12 @@ async function writeRunReceiptAndRollup(
   // Rollup UPSERT: ALWAYS fire so doctor's extract_health sees the
   // cycle ran (even no-op runs are signal — they prove the extractor
   // was alive). Best-effort per F-OUT-19.
-  const incomplete = halted || result.pages_failed > 0;
   await upsertExtractRollup(engine, {
     kind: 'facts.conversation',
     source_id: sourceId,
     cost_delta: result.spent_usd ?? 0,
-    round_completed_delta: incomplete ? 0 : 1,
-    halt_delta: incomplete ? 1 : 0,
+    round_completed_delta: halted ? 0 : 1,
+    halt_delta: halted ? 1 : 0,
   });
 }
 
@@ -1764,11 +1381,6 @@ export async function runExtractConversationFacts(
     pages_skipped: 0,
     pages_skipped_too_large: 0,
     pages_skipped_disappeared: 0,
-    pages_skipped_completed: 0,
-    pages_skipped_non_extractable: 0,
-    pages_marked_non_extractable: 0,
-    pages_failed: 0,
-    pages_llm_fallback: 0,
     pages_lock_skipped: 0,
     orphan_facts_cleaned: 0,
     segments_processed: 0,
@@ -1809,11 +1421,6 @@ export async function runExtractConversationFacts(
       aggregate.pages_skipped += perSource.pages_skipped;
       aggregate.pages_skipped_too_large += perSource.pages_skipped_too_large;
       aggregate.pages_skipped_disappeared += perSource.pages_skipped_disappeared;
-      aggregate.pages_skipped_completed += perSource.pages_skipped_completed;
-      aggregate.pages_skipped_non_extractable += perSource.pages_skipped_non_extractable;
-      aggregate.pages_marked_non_extractable += perSource.pages_marked_non_extractable;
-      aggregate.pages_failed += perSource.pages_failed;
-      aggregate.pages_llm_fallback += perSource.pages_llm_fallback;
       aggregate.pages_lock_skipped += perSource.pages_lock_skipped;
       aggregate.orphan_facts_cleaned += perSource.orphan_facts_cleaned;
       aggregate.segments_processed += perSource.segments_processed;
@@ -1845,21 +1452,6 @@ export async function runExtractConversationFacts(
   if (aggregate.pages_skipped_disappeared > 0) {
     console.log(`  Skipped ${aggregate.pages_skipped_disappeared} page(s) that disappeared between enumeration and fetch.`);
   }
-  if (aggregate.pages_skipped_completed > 0) {
-    console.log(`  Skipped ${aggregate.pages_skipped_completed} page(s) with fresh durable completion outcomes.`);
-  }
-  if (aggregate.pages_skipped_non_extractable > 0) {
-    console.log(`  Skipped ${aggregate.pages_skipped_non_extractable} page(s) previously scanned as not extractable.`);
-  }
-  if (aggregate.pages_marked_non_extractable > 0) {
-    console.log(`  Marked ${aggregate.pages_marked_non_extractable} page(s) as scanned, not extractable.`);
-  }
-  if (aggregate.pages_failed > 0) {
-    console.error(`  Failed ${aggregate.pages_failed} page(s); they remain unfinished and will retry.`);
-  }
-  if (aggregate.pages_llm_fallback > 0) {
-    console.log(`  Parsed ${aggregate.pages_llm_fallback} page(s) with the opt-in LLM fallback.`);
-  }
   if (aggregate.pages_lock_skipped > 0) {
     console.log(`  Skipped ${aggregate.pages_lock_skipped} page(s) held by another worker / process (will retry next run).`);
   }
@@ -1876,9 +1468,6 @@ export async function runExtractConversationFacts(
   // anyBudgetExhausted doesn't trigger exit 3; the budget message
   // above already tells the user what to do, and exit 0 is the right
   // signal for "ran to the cap intentionally."
-  if (aggregate.pages_failed > 0) {
-    process.exit(1);
-  }
   if (aggregate.pages_lock_skipped > 0 && !anyBudgetExhausted) {
     process.exit(3);
   }

src/commands/extract.ts

@@ -35,7 +35,7 @@ import type { BrainEngine, LinkBatchInput, TimelineBatchInput } from '../core/en
 import type { PageType } from '../core/types.ts';
 import { parseMarkdown } from '../core/markdown.ts';
 import {
-  extractPageLinks, parseTimelineEntries, deriveTimelineAnchor, inferLinkType, makeResolver,
+  extractPageLinks, parseTimelineEntries, inferLinkType, makeResolver,
   extractFrontmatterLinks, isGlobalBasenameEnabled, LINK_EXTRACTOR_VERSION_TS,
   WIKILINK_BASENAME_LINK_TYPE,
   buildBasenameIndex, queryBasenameIndex, stripCodeBlocks,
@@ -433,10 +433,7 @@ export async function extractLinksFromFile(
       async resolve(name: string, dirHint?: string | string[]): Promise<string | null> {
         if (!name) return null;
         const trimmed = name.trim();
-        // Same broadened slug-shape as makeResolver step 1: accepts
-        // digit-leading folders (`90-people/nicolai`) and nested paths.
-        // Exact Set membership guards it — no false positives.
-        if (/\//.test(trimmed) && /^[a-z0-9][a-z0-9/_-]*$/.test(trimmed) && allSlugs.has(trimmed)) {
+        if (/^[a-z][a-z0-9-]*\/[a-z0-9][a-z0-9-]*$/.test(trimmed) && allSlugs.has(trimmed)) {
           return trimmed;
         }
         const hints = Array.isArray(dirHint) ? dirHint : (dirHint ? [dirHint] : []);
@@ -585,17 +582,6 @@ export interface ExtractOpts {
    * before (single-'default'-source brains unaffected).
    */
   sourceId?: string;
-  /**
-   * v0.42 — also extract frontmatter links on the incremental (slugs) path.
-   * `extractForSlugs` extracts BODY links only by default; set this true to also
-   * parse each changed page's frontmatter so `sources:`/`related:` edges stay fresh
-   * when YAML is edited externally and synced in. Applied PER changed page, so the
-   * incremental walk stays bounded (no switch to a full DB scan). Only honored on
-   * the incremental path (`slugs` defined); the full-walk path already covers
-   * frontmatter via its own dispatch. Gated upstream by the config key
-   * `autopilot.incremental_extract_include_frontmatter` (default off).
-   */
-  includeFrontmatter?: boolean;
 }
 
 /**
@@ -634,7 +620,7 @@ export async function runExtractCore(engine: BrainEngine, opts: ExtractOpts): Pr
       // Nothing changed — skip entirely.
       return result;
     }
-    const r = await extractForSlugs(engine, opts.dir, opts.slugs, opts.mode, dryRun, jsonMode, workers, opts.signal, opts.sourceId, opts.includeFrontmatter);
+    const r = await extractForSlugs(engine, opts.dir, opts.slugs, opts.mode, dryRun, jsonMode, workers, opts.signal, opts.sourceId);
     result.links_created = r.links_created;
     result.timeline_entries_created = r.timeline_created;
     result.pages_processed = r.pages;
@@ -749,12 +735,6 @@ export async function runExtract(engine: BrainEngine, args: string[]) {
   // v0.41.18.0 (A11, T8): --from-meetings extracts timeline entries from
   // meeting pages onto each discussed entity. Timeline subcommand only.
   const fromMeetings = args.includes('--from-meetings');
-  // --infer-dates: for pages whose body has NO parseable timeline line, anchor
-  // one entry at the page's computed effective_date (frontmatter / filename date,
-  // never the updated_at fallback). Default OFF for back-compat — comms/calendar
-  // brains opt in to populate timeline from slug/frontmatter dates. DB-source only
-  // (needs the full Page.effective_date, which getPage projects).
-  const inferDates = args.includes('--infer-dates');
   // v0.41.17.0 (T7, D9): --workers N parsed via the shared validator.
   // Honored on the fs-walk inner loops only; DB-source paths stay
   // serial in v0.41.17.0 (see ExtractOpts.workers doc).
@@ -969,7 +949,7 @@ Status (v0.42):
           result.pages_processed = r.pages;
         }
         if (subcommand === 'timeline' || subcommand === 'all') {
-          const r = await extractTimelineFromDB(engine, dryRun, jsonMode, typeFilter, since, { sourceIdFilter, inferDates });
+          const r = await extractTimelineFromDB(engine, dryRun, jsonMode, typeFilter, since, { sourceIdFilter });
           result.timeline_entries_created = r.created;
           result.pages_processed = Math.max(result.pages_processed, r.pages);
         }
@@ -1031,11 +1011,6 @@ async function extractForSlugs(
   signal?: AbortSignal,
   // #1747/#1503: stamp resolved brain source id on batch rows (see ExtractOpts.sourceId).
   sourceId?: string,
-  // v0.42: when true, also extract frontmatter links per changed page so
-  // externally-edited YAML (`sources:`/`related:`) stays fresh on the cycle.
-  // Default false preserves the body-only incremental behavior. Gated upstream
-  // by `autopilot.incremental_extract_include_frontmatter`.
-  includeFrontmatter: boolean = false,
 ): Promise<{ links_created: number; timeline_created: number; pages: number }> {
   // Build the full slug set for link resolution (fast: just readdir, no file reads)
   const allFiles = walkMarkdownFiles(brainDir);
@@ -1050,10 +1025,6 @@ async function extractForSlugs(
   let linksCreated = 0;
   let timelineCreated = 0;
   let pagesProcessed = 0;
-  // #2636: successfully processed pages get their extraction watermark
-  // stamped after the final flush (mode 'all' only — a partial-mode run
-  // hasn't done the full extraction the watermark asserts).
-  const processedRefs: Array<{ slug: string; source_id: string }> = [];
 
   // Issue #972: read the basename flag once per extract run.
   const globalBasename = await isGlobalBasenameEnabled(engine);
@@ -1114,7 +1085,7 @@ async function extractForSlugs(
         const content = readFileSync(fullPath, 'utf-8');
 
         if (doLinks) {
-          const links = await extractLinksFromFile(content, relPath, allSlugs, { globalBasename, includeFrontmatter });
+          const links = await extractLinksFromFile(content, relPath, allSlugs, { globalBasename });
           for (const link of links) {
             if (dryRun) {
               if (!jsonMode) console.log(`  ${link.from_slug} → ${link.to_slug} (${link.link_type})`);
@@ -1142,7 +1113,6 @@ async function extractForSlugs(
         }
 
         pagesProcessed++;
-        if (!dryRun) processedRefs.push({ slug, source_id: sourceId ?? 'default' });
       } catch { /* skip unreadable */ }
       progress.tick(1);
     },
@@ -1150,13 +1120,6 @@ async function extractForSlugs(
 
   await flushLinks();
   await flushTimeline();
-  // #2636: the Dream cycle disables sync's inline extraction and routes
-  // changed slugs through this incremental path — without a stamp here,
-  // those pages never get links_extracted_at and stay permanently visible
-  // to `extract --stale` / doctor. Stamp only after BOTH batches flushed.
-  if (!dryRun && mode === 'all') {
-    await stampExtracted(engine, processedRefs);
-  }
   progress.finish();
 
   if (!jsonMode) {
@@ -1589,7 +1552,7 @@ async function extractTimelineFromDB(
   jsonMode: boolean,
   typeFilter: PageType | undefined,
   since: string | undefined,
-  opts?: { sourceIdFilter?: string; inferDates?: boolean },
+  opts?: { sourceIdFilter?: string },
 ): Promise<{ created: number; pages: number }> {
   // v0.32.8: listAllPageRefs enumerates (slug, source_id) pairs so we can
   // thread sourceId to getPage and addTimelineEntriesBatch. Pre-fix used
@@ -1598,7 +1561,6 @@ async function extractTimelineFromDB(
   // v0.37.7.0 #1204: when sourceIdFilter is set, scope the walk to one
   // source so federated brain users can extract per-source.
   const sourceIdFilter = opts?.sourceIdFilter;
-  const inferDates = opts?.inferDates ?? false;
   const allRefs = sourceIdFilter
     ? (await engine.listAllPageRefs()).filter(r => r.source_id === sourceIdFilter)
     : await engine.listAllPageRefs();
@@ -1638,19 +1600,7 @@ async function extractTimelineFromDB(
     }
 
     const fullContent = page.compiled_truth + '\n' + page.timeline;
-    let entries = parseTimelineEntries(fullContent);
-    // --infer-dates: pages with no in-body timeline line but a trustworthy
-    // content date (frontmatter / filename) get one anchor entry at that date.
-    // Applied ONLY on the zero-entry path so it never shadows a real timeline.
-    if (entries.length === 0 && inferDates) {
-      const anchor = deriveTimelineAnchor({
-        slug,
-        title: page.title,
-        effectiveDate: page.effective_date,
-        effectiveDateSource: page.effective_date_source,
-      });
-      if (anchor) entries = [anchor];
-    }
+    const entries = parseTimelineEntries(fullContent);
 
     for (const entry of entries) {
       if (dryRunSeen) {
@@ -1701,7 +1651,7 @@ async function extractTimelineFromDB(
  * make re-extraction idempotent). EVERY processed page is stamped, including
  * zero-link pages — they WERE processed.
  */
-export async function extractStaleFromDB(
+async function extractStaleFromDB(
   engine: BrainEngine,
   opts: {
     dryRun: boolean;
@@ -1734,17 +1684,9 @@ export async function extractStaleFromDB(
   // Batch mode = pg_trgm + exact only, NO per-name search fallback. The
   // resolution map sees ALL sources so qualified cross-source wikilinks resolve
   // even when --source-id scopes the stale SCAN.
-  //
-  // #2576 bug 1: ALWAYS the real resolver — extractPageLinks's opts gate which
-  // pass runs (`skipFrontmatter` for the frontmatter pass, `globalBasename` for
-  // the issue-#972 bare-wikilink pass). The former `includeFrontmatter ?
-  // resolver : nullResolver` ternary predates #972; the synthetic resolver has
-  // no `resolveBasenameMatches`, so the --stale sweep silently skipped basename
-  // resolution even with `link_resolution.global_basename` enabled, stamping
-  // pages as extracted with their bare wikilinks dropped. Mirrors
-  // extractLinksFromDB (including the codex-[P1] `sourceId` scoping).
-  const resolver = makeResolver(engine, { mode: 'batch', sourceId: sourceIdFilter });
-  const globalBasename = await isGlobalBasenameEnabled(engine);
+  const resolver = makeResolver(engine, { mode: 'batch' });
+  const nullResolver = { resolve: async () => null as string | null };
+  const activeResolver = includeFrontmatter ? resolver : nullResolver;
   const allRefs = await engine.listAllPageRefs();
   const allSlugs = new Set<string>();
   const slugToSources = new Map<string, string[]>();
@@ -1776,8 +1718,7 @@ export async function extractStaleFromDB(
     for (const page of rows) {
       const fullContent = page.compiled_truth + '\n' + page.timeline;
       const extracted = await extractPageLinks(
-        page.slug, fullContent, page.frontmatter, page.type, resolver,
-        { skipFrontmatter: !includeFrontmatter, globalBasename },
+        page.slug, fullContent, page.frontmatter, page.type, activeResolver,
       );
       for (const c of extracted.candidates) {
         const r = resolveCandidateSources(c, page.slug, page.source_id, allSlugs, slugToSources);
@@ -1802,18 +1743,7 @@ export async function extractStaleFromDB(
       // `page.updated_at.toISOString()` — the JS Date is ms-truncated, so the
       // µs-precision DB updated_at stayed strictly greater and the page never
       // cleared on Postgres. Stamping the exact value makes them equal.
-      //
-      // BUT the stamp must also clear the version-staleness clause
-      // (`links_extracted_at < versionTs`). A page whose updated_at predates
-      // versionTs would otherwise be stamped below the threshold and read as
-      // stale forever — a permanent re-extract loop that never clears the lag.
-      // GREATEST(updated_at, versionTs) preserves the race semantics (a real
-      // future edit advances updated_at > versionTs >= stamp → re-extracts)
-      // while lifting old pages to the threshold so they clear.
-      const stampIso = page.updated_at.getTime() >= Date.parse(versionTs)
-        ? page.updated_at_iso
-        : versionTs;
-      processedRefs.push({ slug: page.slug, source_id: page.source_id, extractedAt: stampIso });
+      processedRefs.push({ slug: page.slug, source_id: page.source_id, extractedAt: page.updated_at_iso });
     }
 
     // Flush NON-swallowing (CDX-4): a throw here propagates out of the sweep so