Merge branch 'master' into fix/docs-nonexistent-install-command-3502

* fix(test): make resetGateway restore the test baseline instead of unconfiguring (#3554)

bunfig.toml's legacy-embedding-preload pins the gateway once at process
start to openai:text-embedding-3-large @ 1536, but resetGateway() wiped
that pin to _config = null. The next test file's beforeAll engine-connect
then reconfigured from the SHIPPED default (zembed-1 @ 1280) before the
preload's per-test beforeEach could restore anything, and every 1536-d
fixture in that file failed with `expected 1280 dimensions, not 1536`.
Which file pairs collided depended on shard bin-packing, so adding ANY
test file reshuffled the mines (this is what blocks #3545).

Fix: the preload registers its config as a reset baseline via a new
test-only seam (__setGatewayResetBaselineForTests); resetGateway() clears
all module state as before, then re-applies the baseline. All 93 existing
resetGateway() call sites get the correct behavior with zero edits.
Production is untouched: nothing in src/ calls resetGateway() or the
setter, so the baseline is never registered outside tests and
resetGateway() still fully unconfigures there.

Five tests genuinely need an unconfigured gateway (no_gateway_config
diagnosis, isAvailable=false, the #2590 cold-gateway path, the registry
builtin-default tier); they switch to the new __unconfigureGatewayForTests.
Two files' hand-rolled "restore the legacy pin in afterAll/finally"
workarounds for this exact bug are now redundant and simplified away.

Guard test (test/ai/gateway-reset-baseline.test.ts) pins the contract:
1536/openai immediately after resetGateway(), transports still cleared,
hard-unconfigure still available.

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

* fix(test): restore preload's GBRAIN_AUDIT_DIR instead of deleting it (#3554 sibling)

Same bug class as the gateway fix in this PR: state set once by a bunfig
preload (audit-dir-preload's scratch GBRAIN_AUDIT_DIR), wiped by one
file's cleanup, blast radius decided by shard bin-packing. In shard 6,
test/minions-shell.test.ts (position 12) unconditionally deleted the var
in afterAll; test/audit/audit-dir-preload.test.ts (position 93) then
found it undefined and failed 3 tests — and every file in between wrote
audit fixtures toward the operator's real ~/.gbrain/audit/.

Fix: capture the prior value at file load and conditionally restore it,
the same inline save/restore pattern 11 sibling files already use.
test/e2e/skill-brain-first.test.ts had the identical unconditional
delete in afterEach; fixed the same way. Sweep of every
`delete process.env.GBRAIN_AUDIT_DIR` in test/ confirms all remaining
sites are conditional restores.

Ordered-pair proof (minions-shell.test.ts then
audit/audit-dir-preload.test.ts, one process): 3 fail on master,
43/43 pass with this fix.

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

---------

Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>

docs/architecture/KEY_FILES.md

@@ -396,7 +396,7 @@ per-release `**vX.Y.Z:**` narration — CI enforces this
 - `src/commands/lint.ts` — Page quality linter (catches LLM artifacts, placeholder dates)
 - `src/commands/report.ts` — Structured report saver (audit trail for maintenance/enrichment)
 - `src/core/destructive-guard.ts` — three-layer protection against accidental data loss. `assessDestructiveImpact(engine, sourceId)` counts pages/chunks/embeddings/files for a source. `checkDestructiveConfirmation(impact, opts)` is the fail-closed gate (`--confirm-destructive` required when data is present; `--yes` alone is rejected). `softDeleteSource` / `restoreSource` / `listArchivedSources` / `purgeExpiredSources` drive the source-level archive lifecycle via `sources.archived BOOLEAN`, `archived_at TIMESTAMPTZ`, `archive_expires_at TIMESTAMPTZ`. Page-level analog: `BrainEngine.softDeletePage` / `restorePage` / `purgeDeletedPages` plus `pages.deleted_at TIMESTAMPTZ` and a partial purge index. The MCP `delete_page` op rewires to `softDeletePage`; ops `restore_page` (`scope: write`) and `purge_deleted_pages` (`scope: admin`, `localOnly: true`) round out the surface. Search visibility (`buildVisibilityClause` in `src/core/search/sql-ranking.ts`) hides soft-deleted pages and archived sources from `searchKeyword` / `searchKeywordChunks` / `searchVector` in both engines. The autopilot cycle's `purge` phase calls `purgeExpiredSources` + `engine.purgeDeletedPages(72)` so the 72h TTL is real.
-- `src/commands/pages.ts` — `gbrain pages purge-deleted [--older-than HOURS|Nd] [--dry-run] [--json]` operator escape hatch. Mirror of `gbrain sources purge` for the page-level lifecycle. Hard-deletes pages whose `deleted_at` is older than the cutoff; cascades to content_chunks/page_links/chunk_relations.
+- `src/commands/pages.ts` — `gbrain purge-deleted [--older-than HOURS|Nd] [--dry-run] [--json]` operator escape hatch. Mirror of `gbrain sources purge` for the page-level lifecycle. Hard-deletes pages whose `deleted_at` is older than the cutoff; cascades to content_chunks/page_links/chunk_relations.
 - `src/core/op-checkpoint.ts` — DB-backed checkpoint primitive for long-running ops. Migration v67 introduces `op_checkpoints (op TEXT, fingerprint TEXT, completed_keys JSONB, updated_at TIMESTAMPTZ, PK(op, fingerprint))`. Per-op fingerprint helpers (`embedFingerprint`, `extractFingerprint`, `reindexFingerprint`, `integrityFingerprint`, `purgeFingerprint`) compute `sha8(canonical-JSON(relevant-params))` so re-running with the same params resumes from `completed_keys` and re-running with different params (e.g. `--limit 100` vs `--limit 200`) starts fresh. Cross-worker safe on Postgres (DB row, no file-lock race); PGLite degrades gracefully. Replaces per-op file-backed JSON checkpoints scattered across `import.ts`, `embed.ts`, `reindex.ts`. The 7-day TTL GC runs in the cycle's `purge` phase. All writes (`recordCompleted`, `clearOpCheckpoint`) route through `engine.executeRawDirect` + `withRetry(BULK_RETRY_OPTS)` so they survive Supavisor pool exhaustion, and `recordCompleted` returns `boolean` (banked vs failed-after-retries) — the 9 non-sync consumers keep its REPLACE-into-`completed_keys` semantics. Resumable sync uses the additive `appendCompleted(key, deltaKeys)` / `appendCompletedOnce` (the latter no-retry for the SIGTERM path) which INSERT a delta into the `op_checkpoint_paths` child table (migration v115: `(op, fingerprint, path)` PK, FK to `op_checkpoints` ON DELETE CASCADE) via a single writable-CTE `unnest($3::text[])` write — O(delta), killing the old O(N²) full-set rewrite. `loadOpCheckpoint` returns the `UNION ALL` of legacy `completed_keys` + child-table paths (deduped in JS), so an in-flight upgrade loses nothing. The legacy arm is gated on `jsonb_typeof(completed_keys) = 'array'` so a non-array (scalar) parent row can't make `jsonb_array_elements_text` throw "cannot extract elements from a scalar" and take down the whole union (which would discard the valid child rows and lose all banked progress for the key); a third union arm flags the corruption so the loader logs it once and keeps the child rows. Migration v119 adds the `op_checkpoints_completed_keys_array` CHECK (`jsonb_typeof(completed_keys) = 'array'`) — a DB-enforced, always-on guard that makes the scalar-corruption class structurally impossible going forward; the migration repairs any pre-existing scalar to `'[]'` under `LOCK TABLE ... IN SHARE ROW EXCLUSIVE MODE` and `src/core/schema-embedded.ts` + `src/core/pglite-schema.ts` ship the same CHECK on fresh installs (a loader hit now implies schema drift, a disabled constraint, or an out-of-band writer). `recordCompleted` binds its array through `$3::text::jsonb` (NOT a bare `$3::jsonb`) so postgres.js `.unsafe()` doesn't double-encode `JSON.stringify(sorted)` into the scalar string that CHECK rejects — the #2339 bug that aborted every multi-source sync at the first pin write (PGLite parsed it silently, so it shipped). A DATABASE_URL-gated `test/e2e/op-checkpoint-jsonb-parity.test.ts` (its own CI job) asserts the array shape on real Postgres. `syncFingerprint({sourceId, lastCommit})` keys the sync rows. Pinned by `test/op-checkpoint.test.ts` (incl. delta-append, union read, cascade clear, durable-write boolean, and the scalar-parent guard). `import-checkpoint.ts` was NOT migrated to this primitive — both checkpoint systems coexist without conflict; migrating requires async-propagating 4 sync call sites in `src/commands/import.ts` and rewriting 18 tests, deferred.
 - `src/core/brain-score-recommendations.ts` — pure data layer consumed by both `gbrain doctor --remediation-plan` / `--remediate` and `gbrain features`. `computeRecommendations(checks, opts)` returns `Remediation[]` with stable `id`, content-hash `idempotency_key`, `severity`, `est_seconds`, `est_usd_cost`, `depends_on` (references stable ids, not check names — so plan order is reproducible). `classifyChecks(report)` triages every doctor check three-state into `remediable | human_only | blocked` (`human_only` covers RLS warnings and other human-judgment gates; `blocked` covers dependency chains where a parent check failed). `maxReachableScore(checks)` computes the ceiling for empty/under-configured brains (no entity pages → graph_coverage caps at 70; no embedding key → embedding_coverage caps at 60). Cost estimates pull from `anthropic-pricing.ts` (synthesize/patterns/consolidate) and `embedding-pricing.ts` (embed jobs). Pinned by `test/brain-score-recommendations.test.ts` (~27 cases incl. determinism, content-hash idempotency, DB-backed checkpoint provenance, three-state triage).
 - `src/commands/doctor.ts` extension — `--remediation-plan [--json] [--target-score N]` prints what would run (stable `id`, `idempotency_key`, `severity`, `est_seconds`, `est_usd_cost`, `depends_on`); `--remediate [--yes] [--target-score N] [--max-usd N]` submits each plan step as a Minion job in dependency order, re-checking score between steps. `--target-score N` defaults to 90; refuses to start when target exceeds `maxReachableScore()` and lists what's missing. `--max-usd N` is the cron-safety guard — submission refuses when the plan's `est_total_usd_cost` exceeds the cap. JSON envelope adds a `Check.remediation` field (additive, schema_version unchanged). Pinned by tests in `test/doctor.test.ts`.

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 pages restore`)
+- Automatic rollback (today: manual SQL or `gbrain restore`)
 - LLM-assisted mapping_rules codegen from production data (`gbrain
   schema detect-mappings`; deferred to v0.43+)
 

docs/architecture/schema-packs.md

@@ -214,7 +214,7 @@ gbrain schema downgrade
 
 1. `git revert <merge-commit>` — restores the code.
 2. `gbrain schema downgrade --to gbrain-base` — restores config.
-3. (Optional) `gbrain pages purge-deleted --older-than 0h` — drops
+3. (Optional) `gbrain 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

@@ -19,11 +19,13 @@ entire DB from scratch.
 
 This means:
 
-- **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.
+- **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.
 - **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.
@@ -146,11 +148,9 @@ The promise the rule makes:
 # Snapshot what's there
 gbrain stats > /tmp/before.txt
 
-# 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:
+# 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.
 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 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). |
+| 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). |
 | 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 install voice-agent`
+`gbrain skillpack scaffold voice-agent`
 
 That's it.

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 add_timeline_entry {slug} {
+  gbrain timeline-add {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 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}" \
+            gbrain link <slug> <person_slug>
+            gbrain link <person_slug> <slug>
+            gbrain timeline-add <person_slug> {date} \
+                "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 add_link <slug> <entity_slug>
-            gbrain add_link <entity_slug> <slug>
+            gbrain link <slug> <entity_slug>
+            gbrain 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 add_link <slug> <entity_slug>
-            gbrain add_link <entity_slug> <slug>
+            gbrain link <slug> <entity_slug>
+            gbrain 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 get_links media/youtube/{slug}`. Confirm back-links exist to brain pages for every person and company mentioned in the video.
+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.
 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/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 put_raw_data <entity_slug> \
-        --data '{"sources": {"crustdata": {"fetched_at": "...", "data": {...}}, ...}}'
+    gbrain call put_raw_data \
+        '{"slug": "<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 add_timeline_entry <entity_slug> --entry "Page created via enrichment"
+        gbrain timeline-add <entity_slug> {date} "Page created via enrichment"
     elif path == "UPDATE":
         # Append timeline, update compiled truth ONLY if materially new
-        gbrain add_timeline_entry <entity_slug> --entry "Enriched: {new_signal}"
+        gbrain timeline-add <entity_slug> {date} "Enriched: {new_signal}"
         # Flag contradictions -- don't silently resolve them
 
     # Step 7: Cross-reference the graph
-    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
+    gbrain link <person_slug> <company_slug>       # person -> company
+    gbrain link <company_slug> <person_slug>       # company -> person
+    gbrain 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 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.
+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.
 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 get_links <attendee_slug>,
+                "relevant_deals": gbrain call get_links '{"slug": "<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 add_timeline_entry <sender_slug> \
-                --entry "Email re: {subject}. Key info: {extracted_signal}" \
+            gbrain timeline-add <sender_slug> {date} \
+                "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 add_timeline_entry <entity_slug> \
-                    --entry "{what_was_said_about_them}" \
+                gbrain timeline-add <entity_slug> {date} \
+                    "{what_was_said_about_them}" \
                     --source "email from {sender}, {date}"
 
 # WORKFLOW 4: Scheduling Nudges

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 add_timeline_entry <person_slug> \
-            --entry "Met in '{meeting.title}' on {date}. Key points: ..." \
+        gbrain timeline-add <person_slug> {date} \
+            "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 add_timeline_entry <company_slug> \
-            --entry "Discussed in '{meeting.title}': {what_was_said}" \
+        gbrain timeline-add <company_slug> {date} \
+            "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 add_link <slug> <entity_slug>   # meeting -> entity
-        gbrain add_link <entity_slug> <slug>    # entity -> meeting
+        gbrain link <slug> <entity_slug>   # meeting -> entity
+        gbrain 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 get_links meetings/{date}-{slug}`. Verify back-links exist to all attendee and entity pages.
+4. Run `gbrain call get_links '{"slug": "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/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-page` implicitly writes to
+`~/.gstack` via `.gbrain-source`, `gbrain put` 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-page topics/ai ... --source wiki
+gbrain put topics/ai ... --source wiki
 
 # Or rely on the dotfile / env / CWD match
-cd ~/.gstack && gbrain put-page plans/multi-repo ...
+cd ~/.gstack && gbrain put 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 add_timeline_entry <entity_slug> \
-                --entry "{what_was_said}" \
+            gbrain timeline-add <entity_slug> {date} \
+                "{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
+    pages = gbrain list
     for page in pages:
         mentions = extract_entity_mentions(page.content)
-        existing_links = gbrain get_links <page.slug>
+        existing_links = gbrain call get_links '{"slug": "<page.slug>"}'
         for mention in mentions:
             if mention not in existing_links:
-                gbrain add_link <page.slug> <mention_slug>  # fix broken graph
+                gbrain 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 get_timeline <page.slug>
+        timeline = gbrain 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 get_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 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 get_links <slug>`).
+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>"}'`).
 
 ---
 *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 add_link originals/{slug} <entity_slug>
-            gbrain add_link <entity_slug> originals/{slug}
+            gbrain link originals/{slug} <entity_slug>
+            gbrain 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 get_links originals/ambition-debt`. Confirm cross-links exist to related people, meetings, or other originals.
+3. Run `gbrain call get_links '{"slug": "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 future `gbrain plugin list`.                              |
+| `description`    | string | no       | Shown in a future plugin-listing command.                          |
 
 ## Subagent definition files
 

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 file upload ...`) keep unrestricted filesystem access since
+CLI callers (`gbrain files upload ...`) keep unrestricted filesystem access since
 the user owns the machine.
 
 ## Deployment Options

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

@@ -554,7 +554,7 @@ 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/personal-brain.md

@@ -115,21 +115,21 @@ You can use the same keys across multiple agents.
 
 ## Step 6: Install GBrain
 
-Once OpenClaw is running:
+Once OpenClaw is running, installation is two commands — one in the brain repo, one in the agent workspace:
 
 ```bash
-gbrain install
+# 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
 ```
 
-This installs:
+`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`.
 
-- About 60 skills
-- About 9 skill packs
-- Default brain structure
-- MCP server configuration
-- Supabase connection (for embeddings and search)
+`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.)
 
-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.
+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.
-- `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 `extract_facts` cycle 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." `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)`.
+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)`.
 
 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. `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.
+**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.
 
 **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

@@ -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.
-- `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 `extract_facts` cycle 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." `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)`.
+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)`.
 
 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. `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.
+**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.
 
 **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.
 
@@ -3897,7 +3897,7 @@ 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 file upload ...`) keep unrestricted filesystem access since
+CLI callers (`gbrain files upload ...`) keep unrestricted filesystem access since
 the user owns the machine.
 
 ## Deployment Options

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_page  # already done by the CLI; nothing to add here
+gbrain put  # 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/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 (v0.12.0)
+## Forward note
 
-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.
+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.
 
 ## 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`. Use `gbrain research init`
-to scaffold a new one.
+Recipes are YAML files at `~/.gbrain/recipes/{name}.yaml`. Scaffold a new one by
+copying a built-in recipe file and editing its fields.
 
 ### 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_page people/<slug>`).
+- Check if a brain page exists (`gbrain search "<name>"` or `gbrain get 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_page research/<slug>      # via the put_page operation
+gbrain put 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 pages restore
+  - gbrain 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 pages restore <slug>
+gbrain 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 pages restore <slug>`).
+- Source pages soft-deleted with 72h restore TTL (`gbrain 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 pages restore <slug>` first if rollback is needed.
+- Hard-delete soft-deleted source pages before the 72h restore window. Use `gbrain 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/voice-note-ingest/SKILL.md

@@ -43,8 +43,9 @@ 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 via `gbrain transcription` (Groq
-Whisper by default; OpenAI fallback for audio > 25MB segmented via ffmpeg).
+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 pipeline
 
@@ -52,8 +53,9 @@ Whisper by default; OpenAI fallback for audio > 25MB segmented via ffmpeg).
 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 call
-                 gbrain transcription if no transcript was supplied.
+2. TRANSCRIBE  → Use the agent-provided transcript verbatim, OR
+                 transcribe the audio yourself (see "When to invoke")
+                 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/cli.ts

@@ -55,12 +55,17 @@ 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', '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', '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']);
 // 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',
@@ -1265,6 +1270,20 @@ 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') {

src/core/ai/gateway.ts

@@ -642,8 +642,42 @@ function warnRecipesMissingBatchTokens(): void {
   }
 }
 
-/** Reset (for tests). */
-export function resetGateway(): void {
+/**
+ * Test-only reset baseline (#3554). The bunfig preload
+ * (`test/helpers/legacy-embedding-preload.ts`) pins the gateway to the legacy
+ * OpenAI/1536 config at process start, but `resetGateway()` used to wipe that
+ * pin to `_config = null`. The next test file's engine connect then
+ * reconfigured from the SHIPPED default (zembed-1 @ 1280) and every 1536-d
+ * fixture in that file exploded with `expected 1280 dimensions, not 1536` —
+ * a cross-file mine whose placement depended on shard bin-packing.
+ *
+ * When a baseline factory is registered, `resetGateway()` means "back to the
+ * test baseline" instead of "unconfigured": it clears everything as before,
+ * then re-applies the factory's config via `configureGateway()`. A factory
+ * (not a frozen config) so each re-application captures fresh
+ * `process.env`, matching the preload's original `applyLegacy()` semantics.
+ *
+ * Production is untouched: nothing in `src/` calls `resetGateway()` or this
+ * setter, so in production the baseline is never registered and
+ * `resetGateway()` still fully unconfigures. Same `__*ForTests` seam
+ * convention as `__setEmbedTransportForTests` above.
+ */
+let _resetBaseline: (() => AIGatewayConfig) | null = null;
+
+/**
+ * Register (or clear, with `null`) the config factory that `resetGateway()`
+ * re-applies. Called once by the bunfig test preload.
+ *
+ * @internal exported for tests; not part of the public gateway API.
+ */
+export function __setGatewayResetBaselineForTests(
+  factory: (() => AIGatewayConfig) | null,
+): void {
+  _resetBaseline = factory;
+}
+
+/** Clear every piece of module state. Shared by both reset flavors. */
+function clearGatewayState(): void {
   _config = null;
   _modelCache.clear();
   _shrinkState.clear();
@@ -655,6 +689,33 @@ export function resetGateway(): void {
   _extendedModels.clear();
 }
 
+/**
+ * Reset (for tests). Clears all module state (config, model cache, shrink
+ * state, transports, warned recipes, extended models), then — if a test
+ * baseline is registered — re-applies it so the gateway returns to the
+ * process-wide test default instead of an unconfigured limbo (#3554).
+ */
+export function resetGateway(): void {
+  clearGatewayState();
+  // configureGateway re-clears _modelCache/_shrinkState/_extendedModels and
+  // registers the baseline's models; transports are NOT touched by it, so a
+  // stale test transport can never leak back in through this path.
+  if (_resetBaseline) configureGateway(_resetBaseline());
+}
+
+/**
+ * Reset AND stay unconfigured, ignoring any registered baseline. For the
+ * handful of tests that assert genuine no-gateway behavior
+ * (`no_gateway_config` diagnosis, `isAvailable() === false`, graceful
+ * degradation paths). The preload's per-test beforeEach restores the
+ * baseline before the next test, so this cannot leak across tests.
+ *
+ * @internal exported for tests; not part of the public gateway API.
+ */
+export function __unconfigureGatewayForTests(): void {
+  clearGatewayState();
+}
+
 /**
  * Test-only seam. Replaces the function the gateway calls to embed a
  * sub-batch. Pass `null` to restore the real `embedMany` from the AI SDK.

test/ai/gateway-reset-baseline.test.ts

@@ -0,0 +1,68 @@
+/**
+ * #3554 — resetGateway() must restore the test baseline, not unconfigure.
+ *
+ * The bunfig preload (test/helpers/legacy-embedding-preload.ts) pins the
+ * gateway to openai:text-embedding-3-large @ 1536 at process start and
+ * registers that config as the reset baseline. Before the fix,
+ * resetGateway() wiped the pin to _config = null; the next file's beforeAll
+ * engine-connect then reconfigured from the SHIPPED default (zembed-1 @
+ * 1280) and every 1536-d fixture in that file failed with
+ * `expected 1280 dimensions, not 1536`. Which file pairs collided depended
+ * on shard bin-packing, so adding ANY test file reshuffled the mines.
+ *
+ * These assertions pin the contract so it cannot silently rot again.
+ */
+import { describe, test, expect, afterEach } from 'bun:test';
+import {
+  configureGateway,
+  resetGateway,
+  __unconfigureGatewayForTests,
+  __setChatTransportForTests,
+  getEmbeddingModel,
+  getEmbeddingDimensions,
+  isAvailable,
+} from '../../src/core/ai/gateway.ts';
+
+afterEach(() => resetGateway());
+
+describe('resetGateway baseline restore (#3554)', () => {
+  test('immediately after resetGateway(), the preload baseline is live', () => {
+    resetGateway();
+    expect(getEmbeddingModel()).toBe('openai:text-embedding-3-large');
+    expect(getEmbeddingDimensions()).toBe(1536);
+  });
+
+  test('resetGateway() overwrites a file-local config back to the baseline', () => {
+    configureGateway({
+      embedding_model: 'zeroentropyai:zembed-1',
+      embedding_dimensions: 1280,
+      env: {},
+    });
+    expect(getEmbeddingDimensions()).toBe(1280);
+    resetGateway();
+    expect(getEmbeddingModel()).toBe('openai:text-embedding-3-large');
+    expect(getEmbeddingDimensions()).toBe(1536);
+  });
+
+  test('resetGateway() still clears test transports (no stale transport leaks back)', () => {
+    __setChatTransportForTests(async () => {
+      throw new Error('should have been cleared');
+    });
+    resetGateway();
+    // Baseline config sets no chat key in a keyless env, but the transport
+    // seam itself must be gone: isAvailable('chat') short-circuits to true
+    // whenever a chat transport is installed, so with a hard-unconfigured
+    // gateway it can only be true if the transport survived the reset.
+    __unconfigureGatewayForTests();
+    expect(isAvailable('chat')).toBe(false);
+  });
+
+  test('__unconfigureGatewayForTests() gives a genuinely unconfigured gateway', () => {
+    __unconfigureGatewayForTests();
+    expect(() => getEmbeddingDimensions()).toThrow(/not configured/);
+    expect(isAvailable('embedding')).toBe(false);
+    // And a plain reset brings the baseline back.
+    resetGateway();
+    expect(getEmbeddingDimensions()).toBe(1536);
+  });
+});

test/ai/gateway.test.ts

@@ -2,6 +2,7 @@ import { describe, test, expect, beforeEach, afterAll } from 'bun:test';
 import {
   configureGateway,
   resetGateway,
+  __unconfigureGatewayForTests,
   isAvailable,
   embed,
   getEmbeddingModel,
@@ -55,6 +56,9 @@ describe('gateway.isAvailable (silent-drop regression surface)', () => {
   beforeEach(() => resetGateway());
 
   test('returns false when gateway not configured', () => {
+    // resetGateway() restores the preload's test baseline (#3554); go
+    // genuinely unconfigured for this one assertion.
+    __unconfigureGatewayForTests();
     expect(isAvailable('embedding')).toBe(false);
   });
 

test/docs-cli-commands.test.ts

@@ -0,0 +1,138 @@
+/**
+ * #3502: docs must not reference nonexistent gbrain commands.
+ *
+ * `docs/tutorials/personal-brain.md` shipped a `gbrain install` step for two
+ * months after the command it replaced was retired — every reader hit
+ * "Unknown command: install". This guard scans README.md, docs/, and skills/
+ * for `gbrain <verb>` invocations in code (fenced blocks + inline code spans)
+ * and checks each verb against the live CLI surface: CLI_ONLY, operation
+ * cliHints names (non-hidden), and aliases.
+ *
+ * Deliberately excluded (historical or speculative by design, per CLAUDE.md's
+ * "historical docs are never rewritten" rule):
+ *   - docs/GBRAIN_V0.md               — the v0 spec; documents v0's CLI
+ *   - docs/designs/, docs/plans/      — future/speculative design docs
+ *   - docs/migrations/, skills/migrations/ — per-release migration notes,
+ *     written against that release's CLI
+ *   - docs/UPGRADING_DOWNSTREAM_AGENTS.md — per-release upgrade chronicle
+ *
+ * Heuristics keep prose out: only fenced code + inline spans are scanned,
+ * comment lines and diagram lines are skipped, and the verb must sit in
+ * command position (start of command text, or after a shell operator).
+ */
+import { describe, expect, test } from 'bun:test';
+import { readdirSync, readFileSync, statSync } from 'fs';
+import { dirname, join, relative } from 'path';
+import { CLI_ONLY, cliAliases } from '../src/cli.ts';
+import { operations } from '../src/core/operations.ts';
+
+const ROOT = dirname(import.meta.dir);
+
+const EXCLUDED = [
+  'docs/GBRAIN_V0.md',
+  'docs/UPGRADING_DOWNSTREAM_AGENTS.md',
+  'docs/designs/',
+  'docs/plans/',
+  'docs/migrations/',
+  'skills/migrations/',
+];
+
+/** Known-intentional references to commands that deliberately don't exist. */
+const ALLOWLIST: Record<string, string[]> = {
+  // The doc explains that gbrain does NOT ship this command, on purpose.
+  'docs/guides/rls-and-you.md': ['rls-exempt'],
+};
+
+function validCommands(): Set<string> {
+  const valid = new Set<string>(CLI_ONLY);
+  for (const op of operations) {
+    const name = op.cliHints?.name;
+    if (name && !op.cliHints?.hidden) valid.add(name);
+  }
+  for (const alias of cliAliases.keys()) valid.add(alias);
+  return valid;
+}
+
+function* mdFiles(dir: string): Generator<string> {
+  for (const entry of readdirSync(dir)) {
+    const p = join(dir, entry);
+    if (statSync(p).isDirectory()) yield* mdFiles(p);
+    else if (p.endsWith('.md')) yield p;
+  }
+}
+
+interface CodeLine { code: string; line: number }
+
+/** Fenced-block lines + inline code spans that START with `gbrain `. */
+function codeRegions(text: string): CodeLine[] {
+  const out: CodeLine[] = [];
+  const lines = text.split('\n');
+  let inFence = false;
+  for (let i = 0; i < lines.length; i++) {
+    const l = lines[i];
+    if (/^\s*(```|~~~)/.test(l)) { inFence = !inFence; continue; }
+    if (inFence) {
+      const t = l.trim();
+      if (/^(#|\/\/|--|\*)/.test(t)) continue;        // comment lines
+      if (/[│┌┐└┘├┤─═╔╗╚╝]/.test(l)) continue;        // ASCII-art diagrams
+      out.push({ code: l, line: i + 1 });
+      continue;
+    }
+    for (const m of l.matchAll(/`(gbrain [^`]+)`/g)) out.push({ code: m[1], line: i + 1 });
+  }
+  return out;
+}
+
+/** True when `gbrain` sits at command position (not mid-prose). */
+function commandPosition(prefix: string): boolean {
+  const p = prefix.trimEnd();
+  return p === '' || /[|;&`(={[]$/.test(p) || /\$$/.test(p);
+}
+
+function scan(): string[] {
+  const valid = validCommands();
+  const violations: string[] = [];
+  const files = [
+    join(ROOT, 'README.md'),
+    ...mdFiles(join(ROOT, 'docs')),
+    ...mdFiles(join(ROOT, 'skills')),
+  ];
+  for (const file of files) {
+    const rel = relative(ROOT, file);
+    if (EXCLUDED.some((e) => rel === e || rel.startsWith(e))) continue;
+    const text = readFileSync(file, 'utf-8');
+    for (const { code, line } of codeRegions(text)) {
+      for (const m of code.matchAll(/\bgbrain\s+([A-Za-z][\w-]*)/g)) {
+        const verb = m[1];
+        if (!/^[a-z][a-z0-9_-]{2,}$/.test(verb)) continue;   // flags, <slots>, v0.x
+        if (!commandPosition(code.slice(0, m.index))) continue;
+        if (valid.has(verb)) continue;
+        if (ALLOWLIST[rel]?.includes(verb)) continue;
+        violations.push(`${rel}:${line}: \`gbrain ${verb}\` is not a real command — ${code.trim().slice(0, 90)}`);
+      }
+    }
+  }
+  return violations;
+}
+
+describe('#3502 — docs reference only real gbrain commands', () => {
+  test('every `gbrain <verb>` in README/docs/skills resolves to a live command', () => {
+    const violations = scan();
+    expect(violations).toEqual([]);
+  });
+
+  test('the sanity anchors: install is dead, init/put/skillpack are live', () => {
+    const valid = validCommands();
+    expect(valid.has('install')).toBe(false); // retired v0.36.0.0 — the #3502 bug
+    expect(valid.has('init')).toBe(true);
+    expect(valid.has('put')).toBe(true);
+    expect(valid.has('skillpack')).toBe(true);
+  });
+
+  test('pages + bench are dispatchable (documented surfaces; #2035 bug class)', () => {
+    // `pages` had a live handleCliOnly case but was dropped from CLI_ONLY;
+    // `bench` (bench-publish.ts) was documented but never wired at all.
+    expect(CLI_ONLY.has('pages')).toBe(true);
+    expect(CLI_ONLY.has('bench')).toBe(true);
+  });
+});

test/doctor-ze-checks.test.ts

@@ -143,9 +143,10 @@ describe('checkEmbeddingWidthConsistency', () => {
   });
 
   test('gateway unconfigured: skips with ok', async () => {
-    // Reset gateway so requireConfig() throws.
-    const { resetGateway } = await import('../src/core/ai/gateway.ts');
-    resetGateway();
+    // Hard-unconfigure so requireConfig() throws — resetGateway() would
+    // restore the preload's test baseline (#3554).
+    const { __unconfigureGatewayForTests } = await import('../src/core/ai/gateway.ts');
+    __unconfigureGatewayForTests();
     const check = await checkEmbeddingWidthConsistency(engine);
     expect(check.status).toBe('ok');
     expect(check.message).toContain('gateway not configured');

test/e2e/skill-brain-first.test.ts

@@ -81,6 +81,11 @@ function copyFixturesIntoTempWorkspace(): Workspace {
 
 let workspace: Workspace;
 
+// Restore (not delete) after each test: the audit-dir preload sets
+// GBRAIN_AUDIT_DIR once at process start, and deleting it leaks the
+// operator's real ~/.gbrain/audit/ to every later file in the shard.
+const priorAuditDir = process.env.GBRAIN_AUDIT_DIR;
+
 beforeEach(() => {
   workspace = copyFixturesIntoTempWorkspace();
   // Redirect audit dir to the tempdir so the snapshot file doesn't pollute
@@ -89,7 +94,8 @@ beforeEach(() => {
 });
 
 afterEach(() => {
-  delete process.env.GBRAIN_AUDIT_DIR;
+  if (priorAuditDir === undefined) delete process.env.GBRAIN_AUDIT_DIR;
+  else process.env.GBRAIN_AUDIT_DIR = priorAuditDir;
   workspace.cleanup();
 });
 

test/embed-preflight.test.ts

@@ -6,7 +6,11 @@
  * process.env.
  */
 import { describe, test, expect, beforeEach, afterAll } from 'bun:test';
-import { configureGateway, resetGateway } from '../src/core/ai/gateway.ts';
+import {
+  configureGateway,
+  resetGateway,
+  __unconfigureGatewayForTests,
+} from '../src/core/ai/gateway.ts';
 import {
   validateEmbeddingCreds,
   formatEmbeddingCredsError,
@@ -22,18 +26,12 @@ import type { AIGatewayConfig } from '../src/core/ai/types.ts';
 // isAvailable('embedding') check. That's what made facts-backstop-gating
 // fail intermittently (bin-pack-dependent) on CI shard 10.
 //
-// Don't end on a bare resetGateway() either: the NEXT file's beforeAll
-// (often engine.initSchema, which sizes vector columns from ambient gateway
-// state) runs before the legacy-embedding-preload's per-test restore, so a
-// null gateway here would seed 1280-d schemas under 1536-d fixtures.
-// Restore the preload's legacy pin instead.
+// #3554: resetGateway() now restores the preload's legacy pin itself (the
+// preload registers it via __setGatewayResetBaselineForTests), so a bare
+// reset is safe here — the NEXT file's beforeAll sees the 1536-d baseline,
+// not a null gateway that would seed 1280-d schemas under 1536-d fixtures.
 afterAll(() => {
   resetGateway();
-  configureGateway({
-    embedding_model: 'openai:text-embedding-3-large',
-    embedding_dimensions: 1536,
-    env: { ...process.env },
-  });
 });
 
 function baseConfig(overrides: Partial<AIGatewayConfig> = {}): AIGatewayConfig {
@@ -138,7 +136,9 @@ describe('validateEmbeddingCreds', () => {
   });
 
   test('throws no_gateway_config when gateway was not configured', () => {
-    // resetGateway() in beforeEach already cleared _config.
+    // resetGateway() restores the preload's test baseline (#3554), so this
+    // test needs the hard variant to get a genuinely unconfigured gateway.
+    __unconfigureGatewayForTests();
     let caught: unknown;
     try { validateEmbeddingCreds(); } catch (e) { caught = e; }
     expect(caught).toBeInstanceOf(EmbeddingCredentialError);

test/foreground-chat-gateway-init.serial.test.ts

@@ -9,7 +9,11 @@ import { afterEach, beforeEach, describe, expect, spyOn, test } from 'bun:test';
 import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
-import { isAvailable, resetGateway } from '../src/core/ai/gateway.ts';
+import {
+  __unconfigureGatewayForTests,
+  isAvailable,
+  resetGateway,
+} from '../src/core/ai/gateway.ts';
 import { runExtractConversationFacts } from '../src/commands/extract-conversation-facts.ts';
 import { runEnrich } from '../src/commands/enrich.ts';
 
@@ -27,7 +31,10 @@ beforeEach(() => {
   }));
   process.env.GBRAIN_HOME = home;
   process.env.OPENAI_API_KEY = 'test-key';
-  resetGateway();
+  // Hard-unconfigure: this suite exists to exercise the COLD-gateway path
+  // (#2590), and resetGateway() now restores the preload's test baseline
+  // (#3554), which would make configureGatewayIfUninitialized a no-op.
+  __unconfigureGatewayForTests();
 });
 
 afterEach(() => {

test/helpers/legacy-embedding-preload.ts

@@ -18,7 +18,11 @@
  * `configureGateway()` explicitly in their own beforeAll, which
  * overwrites this preload.
  */
-import { configureGateway, getEmbeddingDimensions } from '../../src/core/ai/gateway.ts';
+import {
+  configureGateway,
+  getEmbeddingDimensions,
+  __setGatewayResetBaselineForTests,
+} from '../../src/core/ai/gateway.ts';
 import { beforeEach } from 'bun:test';
 
 const LEGACY_CONFIG = {
@@ -26,12 +30,16 @@ const LEGACY_CONFIG = {
   embedding_dimensions: 1536,
 } as const;
 
-function applyLegacy() {
-  configureGateway({
+function legacyGatewayConfig() {
+  return {
     embedding_model: LEGACY_CONFIG.embedding_model,
     embedding_dimensions: LEGACY_CONFIG.embedding_dimensions,
     env: { ...process.env },
-  });
+  };
+}
+
+function applyLegacy() {
+  configureGateway(legacyGatewayConfig());
 }
 
 if (process.env.GBRAIN_DEBUG_PRELOAD === '1') {
@@ -41,6 +49,16 @@ if (process.env.GBRAIN_DEBUG_PRELOAD === '1') {
 // Initial application — covers tests that don't reset the gateway.
 applyLegacy();
 
+// #3554: make resetGateway() mean "back to this baseline" instead of
+// "unconfigured". Without this, a file whose teardown calls resetGateway()
+// leaves _config = null; the NEXT file's beforeAll engine-connect then
+// reconfigures from the shipped default (zembed-1 @ 1280) BEFORE the
+// beforeEach below can fire, and the 1280-sized schema rejects the file's
+// 1536-d fixtures. Which file pairs collide depends on shard bin-packing,
+// so adding any test file reshuffles the mines. A factory (not a frozen
+// config) so each re-application captures fresh process.env.
+__setGatewayResetBaselineForTests(legacyGatewayConfig);
+
 // Per-test re-application — handles tests that call `resetGateway()`
 // in their setup/teardown. Bun's preload allows registering global
 // hooks; this fires before every test in every file in the shard.

test/llm-intent-escalation.test.ts

@@ -15,6 +15,7 @@ import {
 } from '../src/core/search/llm-intent.ts';
 import {
   __setChatTransportForTests,
+  __unconfigureGatewayForTests,
   configureGateway,
   resetGateway,
 } from '../src/core/ai/gateway.ts';
@@ -122,7 +123,9 @@ describe('classifyModalityWithLLM — fail-open', () => {
   });
 
   test('Gateway not configured → returns fallback', async () => {
-    resetGateway();
+    // Hard-unconfigure: resetGateway() would restore the preload's test
+    // baseline (#3554), whose {...process.env} could make chat available.
+    __unconfigureGatewayForTests();
     // No configureGateway called → isAvailable('chat') returns false.
     expect(await classifyModalityWithLLM('q', 'text')).toBe('text');
   });

test/minions-shell.test.ts

@@ -282,12 +282,19 @@ describe('shell-audit: computeAuditFilename', () => {
 
 describe('shell-audit: write', () => {
   let tmpDir: string;
+  // #3554-sibling: the audit-dir preload sets GBRAIN_AUDIT_DIR once at
+  // process start; deleting it here (instead of restoring) let every file
+  // AFTER this one in the shard write audit fixtures to the operator's
+  // real ~/.gbrain/audit/ — and failed audit-dir-preload.test.ts whenever
+  // bin-packing placed it later in the shard. Restore the prior value.
+  const priorAuditDir = process.env.GBRAIN_AUDIT_DIR;
   beforeEach(() => {
     tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'shell-audit-test-'));
     process.env.GBRAIN_AUDIT_DIR = tmpDir;
   });
   afterAll(() => {
-    delete process.env.GBRAIN_AUDIT_DIR;
+    if (priorAuditDir === undefined) delete process.env.GBRAIN_AUDIT_DIR;
+    else process.env.GBRAIN_AUDIT_DIR = priorAuditDir;
   });
 
   test('GBRAIN_AUDIT_DIR env override resolves to the custom dir', () => {

test/v0_37_fix_wave.serial.test.ts

@@ -55,24 +55,20 @@ describe('v0.37 Lane A — defaults sweep', () => {
   test('A.5: embedding-column registry builtin defaults to ZE/1280 on empty config + gateway', async () => {
     // The registry's resolution chain is cfg > gateway > DEFAULT. With
     // no cfg AND no gateway, it should fall through to the canonical
-    // default (ZE/1280). Reset gateway first to exercise that path.
-    const { resetGateway } = await import('../src/core/ai/gateway.ts');
+    // default (ZE/1280). Hard-unconfigure first to exercise that path —
+    // resetGateway() would restore the preload's 1536 baseline (#3554).
+    const { __unconfigureGatewayForTests, resetGateway } = await import('../src/core/ai/gateway.ts');
     const { getEmbeddingColumnRegistry } = await import('../src/core/search/embedding-column.ts');
-    resetGateway();
+    __unconfigureGatewayForTests();
     try {
       const reg = getEmbeddingColumnRegistry({ engine: 'pglite' } as any);
       expect(reg['embedding']).toBeDefined();
       expect(reg['embedding'].provider).toBe('zeroentropyai:zembed-1');
       expect(reg['embedding'].dimensions).toBe(1280);
     } finally {
-      // Re-apply legacy preload defaults so the rest of the file's tests
-      // (and subsequent files in this shard) see a configured gateway.
-      const { configureGateway } = await import('../src/core/ai/gateway.ts');
-      configureGateway({
-        embedding_model: 'openai:text-embedding-3-large',
-        embedding_dimensions: 1536,
-        env: { ...process.env },
-      });
+      // Restore the preload's legacy baseline so the rest of the file's
+      // tests (and subsequent files in this shard) see a configured gateway.
+      resetGateway();
     }
   });