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Garry TanandClaude Fable 5 99dd1a083c v0.45.5.0 feat(autopilot): brain currency — honest daemon health, migrate quiesce fence, keyless scheduler chain (#4030) 
* docs(designs): agent-bootstrap plan + design docs (normative, review-absorbed)

The scrubbed, in-repo sources of truth for the gbrain bootstrap wave:
AGENT_BOOTSTRAP_DESIGN.md (product scope/sequencing) and
AGENT_BOOTSTRAP_PLAN.md (implementation; all review-finding IDs inlined).

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

* feat(bootstrap): format spec, question bank, identity templates, bundled assets

agent.json manifest (format_version 1, initialized sentinel) + machine-local
install receipt [CX2-1, CX2-12]; 12-question/6-required interview bank with
consent keys and a persist:false sink for the optional provider key [CX2-13];
ten {{TOKEN}} identity templates (generic, adapted to gbrain ops — gates call
recall/query/put_page, write-through-ops rule, keyless agent-authored facts,
silence contract); assets embedded compiled-binary-safe via file-type imports
[ENG-6].

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

* feat(bootstrap): runbook, README paste block, bootstrap guide, TODOS entries

BOOTSTRAP_FOR_AGENTS.md (agent-driven install runbook: CLI phase list is the
source of truth, never-invent rules, Codex approvals preflight, keyless posture,
failure-modes table, version stamp for the skew check); README gains the
full-agent paste block pinned to latest-stable inside the Claude Code/Codex
quick start (memory-only tier stays); docs/guides/bootstrap.md carries the full
install/security/consent/degradation/uninstall contract.

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

* docs(designs): spike instrument for the bootstrap wave (build order 0)

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

* feat(bootstrap): interview + render engines

Interview gate with read-back confirm-hash (any later answer change clears the
confirmation — the hostile single-batch case is structurally impossible),
per-answer provenance, caps + escaping at set time, config-sink routing for the
provider key; renderer with hard-fail token sweep, subordinate fencing of
principal input, never-clobber + backups, deterministic minimal mode for the
template repo, scaled byte floors. 58 unit tests.

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

* feat(bootstrap): private-repo lifecycle — repo create, attach, uninstall, run lock

gh-gated private repo creation with API-verified privacy (rate-limit distinct
from public), refuse-foreign-origin with attach as the sanctioned path, atomic
bootstrap mutex (pid liveness + age + token), receipt-keyed uninstall that
never wholesale-deletes the gbrain home and only offers --delete-brain for a
brain it created; read-only PGLite lock probe (never opens the engine).
54 unit tests, injectable exec seam throughout.

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

* feat(release): latest-stable ref, template-repo publish job, bootstrap CI guards

release.yml advances the latest-stable tag only after assets publish (the paste
block's permanent ref — copies in the wild never rot) and gains a PAT-gated
publish-template job verified against the vendored tree; two skip-graceful
guards (sanctioned-ref + runbook stamp; template/token bijection + placeholder
assertion + generator byte-diff) wired into verify; README + runbook re-admitted
to the CI cache hash; vendored deterministic template tree generated.

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

* feat(context): IPC v2 turn_context + 8KB assembly + visibility resolver + session identity

Discriminated-union IPC with handler map, protocol echo (stale-serve detection),
shared-secret gate, server-side source binding, per-kind budgets; turn-context
assembly (reflex pointers + volunteered pages + world-only hot facts) under a
data-not-instructions envelope trimmed to the harness's 10KB hook-output cap;
facts.default_visibility resolved through one helper at all four sites (explicit
caller wins, typos fail closed); typed sessionId threads _meta.session_id into
the hot-memory cache key. 50 new tests; 180 adjacent tests confirmed green.

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

* feat(persistence): secret-scan, gbrain sources push, durability unification

Pattern secret scanner (own runtime allowlist, redacted previews, corpus-write
redaction mode); sources push runs the whole scan→stage→commit→pull→push
sequence under one cross-platform lock (mkdir-atomic, pid+age+token) with a
deny-glob backstop, commit-first divergence-safe pull, refuse-unverifiable
visibility, and push-status telemetry; gbrain-home choke point unifies
GBRAIN_HOME semantics with config (0700); durability is parent-repo-aware and
rotates its push log at 0600. 35 new tests; 200 existing green.

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

* fix(sources): harden/pull gates accept sources inside a parent git repo

The bootstrap workspace registers brain/ (a subdirectory) as the source; the
durability core already resolves the repo root, so the command gates now check
inside-a-repo rather than .git-right-here [CX2-3].

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

* feat(serve): resident maintenance sweep + keyless capability probe

The lock-owning serve process now closes the persistence loop: startup (3s
post-connect, best-effort, unref'd) and idle (10-min quiet intervals through
the injectable timer seam) sweeps run facts-fence reconciliation, deterministic
link/timeline extraction over recent workspace pages, and spend-gated corpus
ingest (skipped keyless — agent-authored fences cover it). gbrain sweep --once
is the trusted CLI seam bootstrap verify uses. Capability probe renders the
honest keyless/keyed report. Full reuse of the cycle extractor + extract cores;
26 new tests, neighbors green.

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

* feat(hooks): engine-free gbrain hook command, settings writers, transcript parser

Four hook events (session-start digest + crashed-session recovery push,
user-prompt turn-context injection under an 800ms deadline and the 10KB cap,
stop buffers, session-end corpus write with redaction/retention/dedup +
best-effort push); structural JSON settings merger keyed by a _gbrain marker
(foreign hooks and permissions survive); dated host-spec registry; Claude Code
.jsonl parser as a spec-target with a scrubbed 7-shape fixture. Heartbeat is
counters-only by construction. 59 tests; zero engine modules in the import
graph.

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

* docs(bootstrap): cross-link the full-agent path from the connection docs

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

* feat(bootstrap): dispatcher, verify, status — the command assembled

gbrain bootstrap {status,interview,render,repo,hooks,verify,uninstall,attach}:
engine-free except verify (owns its engine, in-process sweep — no live-serve
conflict); phase list is the TS source of truth with install.jsonl telemetry
and the support blob; verify's fail-soft check suite covers the real write path
(put_page → write-through file → sweep → graph floor → recall), passes keyless,
persists snapshots, and ends with the first-run tour. cli.ts wired per the
three-touchpoint rule; doctor gains the bootstrap check group (silent on
machines with no bootstrap state). 28 new tests; 353 adjacent green.

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

* docs: KEY_FILES bootstrap cluster + CLAUDE.md dispatcher row (+ build:llms)

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

* test(bootstrap): e2e pins — hook-under-live-serve, attach, degraded modes, compiled binary, Docker harness

The permanent pins: a real serve holds the PGLite lock while the engine-free
hook completes (and a direct engine open provably throws LiveServeLockError);
stale-socket fail-open; machine-2 attach with marker-keyed hook repair;
decline-everything installs verify green with every degradation named; the
compiled binary renders bundled templates in an empty cwd. Offline Docker
harness (networkless, read-only) gated into heavy-tests.

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

* fix(bootstrap): register doctor check categories + system-of-record allow comments

The six bootstrap doctor checks join OPS_CHECK_NAMES; the sweep's batch link/
timeline inserts carry the explicit extract-path allow comments (the sweep IS
the extraction path for workspace pages).

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

* fix(test): shard wedge cap tracks suite growth (1500s -> 1800s)

At ~9000 tests a healthy shard finished at 1466s and two progressing shards
were false-killed at the old cap; 1800s restores ~25% headroom over the
slowest observed healthy shard. Real hangs still hit it.

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

* test(ci): cache-hash policy — README + runbook edits must invalidate [C2]

The old deny-list assertion predates the paste block; README.md and
BOOTSTRAP_FOR_AGENTS.md are policy-doc re-admissions now, so their edits must
change the hash (a paste-block edit shipping under a cached green was the C2
hole).

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

* fix(test): classify post-suite exit-hangs as warn-pass; file the leak forensics

A shard killed by the wedge watchdog with every assigned file started and zero
fail markers did all its work and leaked a handle at exit — pre-existing and
master-reproducible (P1 TODO carries the full bisect forensics). Bun's per-test
timeout turns a hung test into a (fail), so the classifier cannot mask one.

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

* fix(test): shard cap 2400s — the count-balanced heavy shard needs it under contention

Observed: the heavy shard still progressing 22s before an 1800s kill while
siblings finish at 1150-1550s (split balances file count, not weight). Filed
the load-sensitive WAL-repair flake (pre-existing, master's v0.42.75.0 wave).

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

* test(bootstrap): quarantine env-mutating suites to the serial lane

check-test-isolation R1: six new files mutate GBRAIN_HOME/env at module scope —
the serial lane (one process per file) is the guard's prescribed home for them.
All 114 tests pass post-rename.

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

* docs(readme): per-harness install sections — Codex, Claude Code, then OpenClaw/Hermes

Each harness gets its own complete paste-block section (desktop app first,
terminal noted — Claude Code CLI is the identical harness; Codex CLI works
pull-based today); the OpenClaw/Hermes platform path keeps equal weight with
its one-click deploys and INSTALL_FOR_AGENTS block intact; memory-only and
remote-connect tiers consolidated under 'Lighter ways in'. Supersedes the
review's D5 ordering by user direction; stale heading references updated.

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

* docs(readme): Codex as the recommended first step; OpenClaw/Hermes framed as-intended, high-cost

The install section now routes newcomers explicitly: Codex first
(subscription-priced, nothing to deploy), OpenClaw/Hermes as GBrain used the
way it was designed — always on, at real server + API cost.

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

* fix: doc-audit code chasers — broken recovery hints, stale op description, auto_link key

Four small code fixes surfaced by the markdown accuracy audit:
- doctor's auto-RLS recovery hint pointed at `apply-migrations --force-retry 35`,
  which cannot work (--force-retry targets the vX.Y.Z orchestrator registry, not
  the numeric schema MIGRATIONS array). Hint now points at the recreate SQL in
  docs/guides/rls-and-you.md; test pins against regression.
- v0_11_0 migration printed the same broken-mechanism class of hint
  (`config set minion_mode` writes DB config nothing reads); now names
  `apply-migrations --mode` + preferences.json, the real setter.
- submit_job's op description hardcoded a stale handler list; now points at
  registerBuiltinHandlers as the source plus the --follow discovery trick.
- `auto_link` added to KNOWN_CONFIG_KEYS: read by link-extraction, reconcile-links,
  and sweep, and documented as the off-switch in brain-ops/maintain, but the
  allowlist rejected `config set auto_link false`.

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

* docs: repo-wide accuracy + MECE reform from the 9-bucket markdown audit

A code-grounded audit of every markdown file (root, architecture, guides,
mcp, tutorials, docs-root, operations/eval/designs, skills, recipes) followed
by a fix wave with per-bucket ownership. Four classes of change:

Accuracy — every documented command/flag verified against src/ before writing:
dead commands replaced with working ones (pages purge-deleted, jobs watch
--follow, gbrain restore, import-based Obsidian flow, space-separated --scopes,
real thin-client recipes, working isolation verification, real supervisor
restart procedure, curl-based ngrok health check, real minion_mode setter);
count drift fixed with rot-proof phrasing (100+ ops, 50+ bundled skills via
skills/manifest.json, 140+ engine methods, KNOBS_HASH_VERSION pointer instead
of hardcoded versions); stale claims corrected (search-mode defaults, RETRIEVAL
pipeline order incl. autocut, sentinel rules, refusal-list mechanism, engine
snapshot, shard cap 2400s + EXIT-HANG classifier in TESTING.md, latest-stable +
publish-template documented in RELEASING.md as release.yml promises).

MECE — one home per concept, pointers elsewhere: test isolation → TESTING.md;
OAuth registration + --bind/--public-url lore → DEPLOY.md; mode bundles →
guides/search-modes.md (the home the CLAUDE.md dispatcher always promised);
merge contract → schema-packs.md; WAL ladder → ENGINES.md; quiet-hours →
quiet-hours.md; capture taxonomy → entity-detection.md; person-page taxonomy →
compiled-truth.md; brain-first protocol → brain-first-lookup.md; refresh
semantics → refresh-algorithm.md; KEY_FILES.md deduplicated (58 extension
entries merged, one entry per file); infra-layer.md rewritten as a pointer page.

Privacy — placeholder sweep across guides, docs, skills, and recipes per the
iron rule; per-release narration stripped from reference docs (current-state
prose only).

Bootstrap coverage — AGENTS.md pointer, RESOLVER routing row, INSTALL.md path,
tutorial cross-links, keyless-mode sections in spend-controls/headless-install.

skills.lock.json regenerated; llms.txt/llms-full.txt rebuilt. Gates: verify
36/36, typecheck clean, doctor 96/96, skills-integrity + resolver + build-llms
+ config-set + migrations all green.

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

* docs(readme): refresh production-brain stats to current brain-repo counts

155,795 pages / 24,589 people / 5,340 companies, counted from the brain
repo's current HEAD; the "100K-page brain" framing moves to 150K to match.
Cron-fleet count unchanged (its store lives on the deployment host, not in
the repos available for verification).

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

* fix(scan,push): modern OpenAI/Voyage key patterns, scan staged blobs not disk

- secret-scan matches sk-proj-/sk-svcacct-/sk-None- and pa- Voyage keys
  (the bare sk- pattern missed every current OpenAI key format).
- workspacePush stages first, then scans the staged index blobs via
  git cat-file, closing the scan-then-stage TOCTOU where a file changed
  between snapshot and commit shipped unscanned.
- shared binary-sniff helper, memoized glob regexes, atomic push-status
  write, and tests for pull_conflict + gitignored deny-match paths.

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

* fix(ci): regenerate flag registry for new commands, harden shard classifier + release token

- cli-flag-registry.generated.ts regenerated: bootstrap/hook/sweep and
  sources push --message/--allow-unverified-remote were missing, so the
  strict #2185 validator rejected real invocations and skipped the new
  commands entirely.
- EXIT-HANG shard classifier now requires every assigned file to have
  started before warn-passing a watchdog kill (was fail-open).
- release.yml passes TEMPLATE_REPO_PAT via http.extraheader, off the argv.
- compiled-binary e2e fails loud in CI instead of a silent permanent skip.

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

* fix(hook,sweep,ipc): non-blocking hook pushes, bounded sweep + cache, source-bound resolve

- session-start/session-end no longer run synchronous git + inline push
  inside their self-deadline; a detached child does the push and the hook
  returns immediately (blocked Claude Code startup for minutes on a dirty
  tree before).
- serve sweep drops the unbounded listAllPageRefs, resolves only candidate
  targets, claims corpus files atomically (no double-LLM-spend race), and
  caps the fence LIKE scan; heartbeat writes are O_APPEND with rare compaction.
- hot-memory cache evicts expired entries and bounds entry count (the key is
  caller-controlled via _meta.session_id).
- v1 resolve IPC honors boundSourceId like turn_context; turn-context runs
  its arms concurrently. doctor reads push/heartbeat thresholds from hook.ts.
- new tests: doctor bootstrap checks, hook push-gate + deadline, concurrent
  sweep claims, cache eviction, bound-source resolve.

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

* fix(bootstrap): origin-ownership gate, world visibility, collision-safe source id, consent + templates

- repo adoption requires an exact receipt repo_url match or authed-owner
  check (undefined repo_url was a wildcard); create verifies privacy BEFORE
  the first push.
- verify sets facts.default_visibility=world if unset, so agent-authored
  facts surface in per-turn context (they defaulted private before).
- source_id derives a path-hash suffix when 'workspace' is taken by another
  checkout; every consumer reads manifest.source_id.
- skipped HOOKS_CONSENT now declines (was falling through to default yes);
  --minimal refuses on an initialized manifest; tilde fences escaped.
- MCP registration pins --surface full; status hard-fails a public origin
  (template door); receipt writers guard against newer/corrupt receipts;
  uninstall only claims brain-deleted after a real rm.
- templates ship jobs disabled + provider-consent + support-relay lines;
  soul-audit re-runs over the shared interview bank. TODOS: 11 follow-ups.

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

* fix(security): close adversarial-review findings — scan fails closed, whole-PEM redaction, bound repo push

Cross-model adversarial pass (Claude + Codex) on the bootstrap wave:

- secret scan fails CLOSED: an unreadable, oversized, or binary staged blob
  now blocks the push (blocked_unscannable, exit 5) instead of committing
  unscanned; only a confirmed staged deletion is skipped. This was the
  headline "block secrets before they leave the machine" property failing open.
- private-key redaction spans the whole PEM block (header+body+footer), not
  just the header line — the base64 body no longer survives into the corpus
  the sweep sends to an extraction provider.
- bootstrap repo commits the workspace (secret-scan-gated) before the first
  push and verifies the remote actually received it, so a push-fail retry
  can't adopt an empty remote as success.
- privacy verify is re-bound to origin immediately before push (a concurrent
  origin rewrite between verify and push is refused).
- session-end corpus write is atomic and clears the stale ingested/in-progress
  sidecars so a resumed session's appended transcript is re-ingested.
- public-origin refusal enforced at render (not only status); MCP "already
  registered" is verified to target this workspace, not blessed blindly;
  verify probe cleanup scopes deletes to its own slugs, not a token substring;
  allowlist fingerprint floor raised 8→16 hex.

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

* v0.45.0.0 feat(bootstrap): paste-in personal-agent install for Codex + Claude Code

Turns a Codex or Claude Code session into a persistent personal agent:
interview-rendered identity files, a local PGLite brain, per-turn context via
serve IPC (Claude Code hooks / Codex pull protocol), session-triggered
persistence, and a private GitHub repo as the agent's portable body. Keyless-
first (the harness model is the LLM; one optional key adds embeddings +
extraction). New `gbrain bootstrap` command family + `gbrain hook` + `gbrain
sweep`; doctor bootstrap health checks; latest-stable distribution ref +
template-repo publish job. Opt-in, additive — existing installs untouched.

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

* fix: regenerate flag registry for security-fix flags; drop fabricated gbrain capabilities doc ref

CI caught two real failures under the merged state:
- the flag registry lagged the blocked_unscannable/exit-5 flags the security
  round added, tripping the #2185 freshness guard.
- headless-install.md described the keyless capability report as a
  `gbrain capabilities` command, which the #3502 doc-command resolver
  rejects — reworded to prose (the real surface is bootstrap verify's report).

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

* docs: sync KEY_FILES + bootstrap plan to security-fix behavior

Cross-referenced the security-fix round against the reference docs and
corrected the drift those commits introduced:

- workspace-push.ts entry: stage-FIRST-then-scan order (the TOCTOU fix),
  fail-closed blocked_unscannable, and the sources-push status -> exit-code map.
- hooks.ts entry: MCP registration pins `serve --surface full`.
- hook.ts entry: session-start/session-end pushes run in a detached child
  (non-blocking); atomic corpus write clears stale sidecars.
- bootstrap.ts entry: render hard-refuses a public origin (template door).
- verify.ts entry: source_id collision resolution (workspace-<path-hash>).
- AGENT_BOOTSTRAP_PLAN as-shipped delta note for the scan/stage reorder.

llms bundle unchanged (KEY_FILES is link-only); build:llms and
test/build-llms.test.ts green.

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

* fix(ci): silence SC2016 on the intentional askpass literal in release.yml

The one-shot GIT_ASKPASS script must contain literal $1 and
$TEMPLATE_REPO_PAT so they expand when /bin/sh runs it at git's credential
prompt, not when the outer shell writes the file — single quotes are correct.
Add a scoped shellcheck disable so actionlint passes.

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

* fix(skills): declare 'bootstrap my data' trigger in cold-start frontmatter

The doc reform added 'bootstrap my data' to cold-start's RESOLVER.md row (to
disambiguate data-bootstrap from agent-bootstrap) but not to the skill's own
frontmatter triggers, tripping the RESOLVER↔frontmatter round-trip contract
(resolver.test.ts). Declare it; regenerate skills.lock.json.

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

* feat(bootstrap): default per-turn hooks + search mode ON without a prompt

Installing gbrain for your coding agent IS the consent for the behaviors that
make it work, so stop re-litigating them with install-time questions whose
"no" defeats the product:

- Per-turn hooks (Claude Code) install ON by default — no prompt. Off-ramps:
  `--no-hooks` at install, `GBRAIN_HOOKS=0` at runtime, `bootstrap uninstall`.
  The "hooks installed" line now surfaces the kill switch so default-on is
  never silent. A persisted HOOKS_CONSENT=no (interview --skip) still declines.
- Search mode defaults to `balanced` silently (nobody knows the modes at
  install; `gbrain search modes` changes it any time).
- MCP scope stays the ONE deliberate prompt — project vs user is a real
  cross-repo privacy choice, not friction.

Marks the two consents `silent: true` in the question bank (new QuestionSpec
field), rewrites the runbook phases so the agent no longer asks them, adds the
`--no-hooks` flag (+ registry regen), and adds default-on / opt-out tests.

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

* test(bootstrap): real end-to-end coverage — cross-session recall, per-turn content, Codex door, realistic corpus

Closes the seven e2e gaps a coverage audit surfaced: the plumbing was
well-unit-tested but the product claims ("Codex works, context shows up every
turn with real content, it remembers across restarts, machine two recovers,
Postgres works") were unproven end to end. Test-only wave — zero src changes.

- Hermetic synthetic corpus (test/fixtures/bootstrap-corpus/ + a loader helper):
  12 interlinked pages (52 edges, timelines), 12 world/private beliefs, 8 gold
  queries — curated from the gbrain-evals synthetic corpora, 100% placeholder
  names, so recall is asserted on a real multi-entity brain instead of a
  2-node self-planted probe.
- GAP1 magic moment: author a fact via the real write path, disconnect the
  engine, reopen against the same DB, recall it — a real session boundary, not
  verify.ts's same-connection SQL read-back. Plus a source-isolation assertion.
- GAP2 per-turn content: hook-under-serve Pin 1 now seeds a known fact and
  asserts its text lands in the injected block AND private beliefs never do
  (was: empty brain, empty_block accepted as a pass).
- GAP3 Codex door: assert the rendered AGENTS.md carries the Gate-3 brain-first
  pull protocol; make the fake codex shim implement `mcp get` so the [FIX7]
  target-verification can actually fail; the Docker cold-machine harness now
  exercises the hooks/MCP registration step instead of skipping it.
- GAP4 corpus recall: turn-context + verify graph-floor/qrels run on the real
  multi-entity brain with real edges.
- GAP5 attach: machine-two now re-ingests the cloned brain/ into a fresh DB and
  recalls a fact authored only on machine one — the multi-device payoff.
- GAP6 keyed + Postgres (env-gated): real embeddings prove semantic recall a
  paraphrase query can reach but keyless BM25 cannot; bootstrap verify drives a
  real Postgres engine (skipIf DATABASE_URL/keys absent).
- GAP7 persistence: session-end runs the REAL push (not the mocked seam) to a
  local bare remote and the remote receives the content; a planted secret is
  blocked at the gate; the 15-min cron installs and fires a scan-gated push.

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

* test(bootstrap): real-agent e2e — drive the actual claude + codex binaries end to end

Closes the audit's biggest gap ("no real harness ever drives a turn"). Adapts
gstack's PTY/headless agent harness to prove the bootstrap install + smoke work
against the REAL binaries, not PATH shims. Test/CI/docs only — zero src changes.

- test/helpers/agent-harness.ts: hermetic clean-room child env (ported from
  gstack; drops CONDUCTOR_/CLAUDE_/GSTACK_/MCP_/GBRAIN_, promotes
  GSTACK_ANTHROPIC_API_KEY→ANTHROPIC_API_KEY), real-binary resolvers + auth
  probes, headless `claude -p --output-format stream-json` and `codex exec
  --json` turn runners, a gbrain stdio MCP-config writer, and a keyless brain
  seeder. + a fixture-parse unit test (no binary needed).
- test/e2e/bootstrap-real-claude.serial.test.ts: real `gbrain bootstrap`
  install → REAL `claude mcp add` (verified via `claude mcp get`) → verify
  exit 0 → a real `claude -p --mcp-config --strict-mcp-config` turn that
  invokes mcp__gbrain__search and answers from the brain (proven: toolCalls
  include mcp__gbrain__search, final text carries the seeded fact).
- test/e2e/bootstrap-real-codex.serial.test.ts: same install with REAL `codex
  mcp add` into a real ~/.codex/config.toml + Gate-3 pull-protocol assertion,
  then a real `codex exec --json` turn surfacing the fact (MCP or the pull-
  protocol shell path). Bounded retry absorbs codex's occasional MCP-call
  cancellation without softening the fact-requiring assertion.
- Everything hermetic (temp HOME/CLAUDE_CONFIG_DIR/CODEX_HOME/GBRAIN_HOME;
  real ~/.codex auth copied read-only) and skipIf-gated so it self-skips
  cleanly where the binaries/auth are absent.
- heavy-tests.yml: gated `real-agent-e2e` job (nightly/label, never the PR
  shard; no-op on a runner without authed binaries).
- TODOS: compiled `gbrain` binary can't serve a PGLite brain (bun compile
  omits the WASM/extension payloads); harness falls back to `bun run` serve.

Verified against live claude 4.6 + codex 0.147.0: 15 pass / 0 fail; verify
36/36; typecheck clean.

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

* fix(ci): real-agent-e2e job — bash array + --timeout (actionlint SC2086 + bun-test-timeout guard)

The real-agent-e2e job's file loop used an unquoted $FILES (SC2086) and ran
`bun test` without --timeout (check-bun-test-timeout guard). Switch to a bash
array and add --timeout=600000 (real-agent turns are slow; the tests self-skip
without authed binaries so it's a no-op elsewhere).

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

* fix(pglite): embed WASM + extension assets so the compiled binary can serve

A `bun build --compile` gbrain binary could not `serve` a PGLite brain: the
compile bundles JS but not PGLite's runtime payload (pglite.wasm, initdb.wasm,
pglite.data, vector/pg_trgm tarballs), so `serve` on PGLite died with a
bunfs/ENOENT. Now the assets ride inside the binary.

- src/core/pglite-embedded-assets.ts: embeds the five assets via
  `import … with { type: 'file' }` (the ENG-6 idiom) and exposes
  getEmbeddedPgliteOptions() → { pgliteWasmModule, initdbWasmModule, fsBundle,
  extensions:{vector,pg_trgm} }. WASM/fsBundle are consumed as bytes; the two
  extension tarballs are materialized to a content-addressed temp file (atomic,
  size-verified reuse) because PGLite reads them via fs.createReadStream, which
  cannot read a /$bunfs path. Unconditional (works in bun-run and compiled),
  so no fragile mode branch.
- src/core/pglite-engine.ts: static-import getEmbeddedPgliteOptions (engine
  path stays static per the engine-dynamic-import invariant); spread into both
  PGlite.create sites (initial + WAL-repair retry). The bunfs classifier stays
  as a backstop but no longer fires for a correct binary.
- scripts/check-pglite-embedded.sh (+ smoketest): compiles a focused binary and
  asserts it boots PGLite, CREATE EXTENSION vector/pg_trgm, and round-trips a
  page — wired into `bun run verify` (now 37 checks), check:all, and
  check:pglite-embedded. Fail-soft only when compile is unavailable.
- agent-harness.ts probeCompiledPglite now passes → the real-agent e2e uses the
  fast compiled MCP server. TODOS: the P2 "can't serve PGLite" item is closed.

Verified: fresh compiled binary ran `search`/`query` against a PGLite brain and
returned the seeded row (no bunfs/ENOENT); verify 37/37; pglite-engine 120/0
source-mode; typecheck clean; engine-dynamic-import + parity guards pass.

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

* fix(source-health): wall-clock ceiling for content-relative staleness

A source whose stored content timestamp trailed its last sync reported
zero lag forever — the shape that let a dead sync daemon stay invisible
for 71 days. lagFromContentMs now ramps toward stale past a ceiling
(default 72h, GBRAIN_STALENESS_CEILING_HOURS / GBRAIN_SYNC_FRESHNESS_FAIL_HOURS)
instead of returning a flat 0; ramping rather than stepping keeps the
warn tier firing before the fail tier across sync_freshness,
federation_health, and gbrain status. The ceiling resolves once per
report (hoisted out of the per-source loops), and the numeric env
plumbing moves to a shared warn-once resolver (src/core/env-number.ts)
so doctor and source-health share one memo instead of warning twice.
Doctor's wedged-lock alarm prints minutes below one hour so a
fractional ceiling override cannot produce a "held the lock for 0h"
message.

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

* fix(autopilot): heartbeat-truth status, self-disable guard, migrate quiesce fence

Status becomes honest and engine-free: a pure classifier maps heartbeat
age, markers, and install detection to not_installed/disabled/paused/
never_run/stale/fresh with exit codes 0/1/2, dispatched in cli.ts before
connectEngine so a live PGLite daemon's exclusive lock or a DB outage
cannot take down the alarm. Tolerance is six intervals (the adaptive
scheduler sleeps two between ticks on healthy brains; three flapped
false alarms), NaN-proof at both parse sites, and a cron'd status
monitor line no longer reads as an install.

The generated wrapper self-disables for real when its repo vanishes —
marker first, then supervisor-specific stop (launchctl bootout /
systemctl disable) since a bare exit 0 under KeepAlive is just a quieter
respawn loop — and requires three consecutive misses so a slow-mounting
volume cannot permanently kill a healthy install. Install and uninstall
clear both markers; wrapper artifacts resolve through gbrainHomePath
with GBRAIN_HOME baked in at install time.

gbrain migrate quiesces the whole write plane for its copy window: an
unconditional atomic pause-marker claim doubles as the migration mutex
(a live holder, a foreign hold, or an unwritable marker all abort;
orphan adoption is renameSync compare-and-claim), in-flight writers
drain via the DB lock table plus active-job count (supervisor presence
locks excluded) before enumeration, minion workers stop claiming queued
jobs while the marker is parked, cleanup registers at claim time, the
daemon self-clears a dead migrate's orphan, and after a clean config
flip the daemon detects the engine identity change and relaunches onto
the new engine instead of syncing into the abandoned one indefinitely.
Malformed connection URLs classify as operator config verdicts rather
than crashes, and torn config reads cannot spuriously restart the
daemon.

Marker paths, the launchd label seam, and the pid-ownership primitives
live in the new leaf module src/core/autopilot-paths.ts so migrate and
the worker never import the autopilot command surface (flag-registry
pooling); the regenerated registry reflects the new one-level imports.

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

* fix(embed,sync): keyless stale embed refuses cleanly; typechange statuses; test-home isolation

The documented agent-scheduler chain (sync, then a stale embed) exited 1
on every keyless brain because EmbeddingDisabledError fell through to a
blanket exit. A bare stale run now refuses cleanly via the pure
isKeylessStaleRefusal predicate (stderr hint, zero-failure result);
explicit asks — a slug, a slugs list, the all flag — still exit 1,
mirroring the dispatch precedence where a slugs list wins over stale.

buildSyncManifest handles the T/U/C git statuses instead of silently
dropping them (typechange routes to modified; the file-to-symlink
staleness residual is documented and filed). Status reports gain
hours_since_last_sync so the ceiling-ramped staleness_hours stops
doubling as the human-facing wall-clock number.

The sync-failures ledger honors GBRAIN_SYNC_FAILURES_DIR and the test
preload (bunfig) points it at a scratch dir, so test runs stop writing
failure rows into the developer's real brain home.

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

* test(e2e): real-launchd lifecycle + agent-scheduler contract harness tier

Two serial-lane e2e files that assert behavior, not artifacts: a
launchd lifecycle suite (shimmed supervisor on every platform; REAL
launchd on darwin under a per-run unique label, own-label cleanup only)
driving install, self-disable via three strikes, status exit codes,
reinstall, and uninstall through the actual CLI; and an
agent-scheduler contract suite that runs the documented sync-and-embed
shell chain end-to-end against a keyless brain, including the
pull-failure case that must break the chain and the heartbeat that must
advance on quiet re-runs.

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

* docs: KEY_FILES current-state for the brain-currency wave; BRAIN_CURRENCY design doc

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

* fix(migrate,minions): ownership-conditional pause release + post-claim fence re-check

Round-4 adversarial hardening on the quiesce protocol. Orphan adoption
verifies identity AFTER its atomic rename — a racer that completed the
whole adopt-and-rewrite in the read-to-rename gap gets its live marker
restored no-clobber instead of stolen. Marker release compares content
before unlinking, so a claim that changed hands can never delete the new
owner's fence mid-copy. On the worker side, a job whose claim committed
after migrate's drain probe is released back to the queue un-run
(delayed one minute, conditional on our lock token) instead of executed
into the doomed source engine. The cross-host residual — a worker on
another machine never sees a local marker file — is filed as the
DB-visible-pause follow-up.

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

* test(autopilot): migrate the crontab wrapper-detection pin to the pure seam

The inline crontab.includes check this static pin matched became
crontabIndicatesAutopilotInstall; the pin now exercises the function
directly (wrapper line still detected) and asserts the detect path is
wired through it.

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

* v0.46.0.0 feat(autopilot): brain currency — honest daemon health, migrate quiesce fence, keyless scheduler chain

VERSION + CHANGELOG + TODOS for the brain-currency PR-A wave, plus the
version-stamped bootstrap runbook and vendored template regen.

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

* docs: sync documentation for v0.46.0.0

The brain-currency wave shipped new user-facing surface the guides did not
carry: the trustworthy autopilot --status exit codes (0/1/2 + paused),
the keyless-safe sync-and-embed chain, and the migrate quiesce fence.

- docs/guides/live-sync.md: keyless clean-refusal note on the embed --stale
  primitive; new "gate on the daemon's heartbeat" verify item with the
  exit-code contract.
- docs/guides/cron-schedule.md: the recommended autopilot health-gate cron
  line (the status classifier already special-cases this monitor line so it
  never reads as an install).
- docs/ENGINES.md: migrate --to now documents the pause-marker mutex, worker
  job-pickup fence, DB-lock drain (GBRAIN_MIGRATE_QUIESCE_SECONDS, default
  300), crash-safe release, and daemon relaunch after the flip.
- docs/operations/headless-install.md: keyless mode's "refuse cleanly" claim
  made concrete — the documented chain exits 0 on a bare stale embed.
- INSTALL_FOR_AGENTS.md Step 7: health-gate bullet + keyless-safe chain note.
- skills/maintain/SKILL.md: autopilot check now teaches the exit-code
  semantics and the --json report fields.
- docs/TESTING.md: inventory entries for the two new harness-tier serial
  suites (real-launchd lifecycle, agent-scheduler shell-chain contract).
- llms-full.txt regenerated (TESTING.md is inlined in the bundle).

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

* docs: cross-model doc-review fixes for v0.46.0.0

Round two from the post-ship documentation review, checked against the code:

- CHANGELOG.md: two shipped fixes were missing from the 0.46.0.0 entry
  (git typechange/unmerged statuses no longer dropped by sync; a wedged
  lock holder past the staleness ceiling now fails doctor with the
  break-lock remedy), and the env-resolver bullet over-claimed its
  coverage — narrowed to the doctor + staleness-threshold vars it
  actually serves. Additive + accuracy only; no entries replaced.
- docs/guides/live-sync.md: Tricky Spots item for the staleness
  wall-clock ceiling (GBRAIN_STALENESS_CEILING_HOURS, default 72h,
  ramp-not-step) and the hours_since_last_sync status field.
- docs/ENGINES.md: the quiesce paragraph over-stated marker release —
  now describes the pid-checked orphan adoption, the daemon self-heal
  poll, and the confirm-the-pid manual step for daemonless hosts.
- docs/guides/minions-fix.md: the verify block's bare autopilot --status
  now notes the exit code is the verdict (and the set -e caveat).
- llms-full.txt regenerated.

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

* v0.45.5.0 chore(release): re-version 0.46.0.0 -> 0.45.5.0

Same release content; the version slots into the 0.45.x line per the
natural-next-off-master convention. VERSION, package.json, CHANGELOG
header, bootstrap runbook stamp, vendored template regen, lockfile, and
llms bundles all move together (trio audit green; stamp + template +
llms freshness guards re-run green).

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

* chore(skills): refresh skills.lock version stamp for 0.45.5.0

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

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
 2026-08-12 09:40:57 -07:00
Garry TanandClaude Fable 5 d35c9c9e44 v0.45.0.0 feat(bootstrap): paste-in personal-agent install for Codex + Claude Code (#3975) 
* docs(designs): agent-bootstrap plan + design docs (normative, review-absorbed)

The scrubbed, in-repo sources of truth for the gbrain bootstrap wave:
AGENT_BOOTSTRAP_DESIGN.md (product scope/sequencing) and
AGENT_BOOTSTRAP_PLAN.md (implementation; all review-finding IDs inlined).

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

* feat(bootstrap): format spec, question bank, identity templates, bundled assets

agent.json manifest (format_version 1, initialized sentinel) + machine-local
install receipt [CX2-1, CX2-12]; 12-question/6-required interview bank with
consent keys and a persist:false sink for the optional provider key [CX2-13];
ten {{TOKEN}} identity templates (generic, adapted to gbrain ops — gates call
recall/query/put_page, write-through-ops rule, keyless agent-authored facts,
silence contract); assets embedded compiled-binary-safe via file-type imports
[ENG-6].

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

* feat(bootstrap): runbook, README paste block, bootstrap guide, TODOS entries

BOOTSTRAP_FOR_AGENTS.md (agent-driven install runbook: CLI phase list is the
source of truth, never-invent rules, Codex approvals preflight, keyless posture,
failure-modes table, version stamp for the skew check); README gains the
full-agent paste block pinned to latest-stable inside the Claude Code/Codex
quick start (memory-only tier stays); docs/guides/bootstrap.md carries the full
install/security/consent/degradation/uninstall contract.

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

* docs(designs): spike instrument for the bootstrap wave (build order 0)

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

* feat(bootstrap): interview + render engines

Interview gate with read-back confirm-hash (any later answer change clears the
confirmation — the hostile single-batch case is structurally impossible),
per-answer provenance, caps + escaping at set time, config-sink routing for the
provider key; renderer with hard-fail token sweep, subordinate fencing of
principal input, never-clobber + backups, deterministic minimal mode for the
template repo, scaled byte floors. 58 unit tests.

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

* feat(bootstrap): private-repo lifecycle — repo create, attach, uninstall, run lock

gh-gated private repo creation with API-verified privacy (rate-limit distinct
from public), refuse-foreign-origin with attach as the sanctioned path, atomic
bootstrap mutex (pid liveness + age + token), receipt-keyed uninstall that
never wholesale-deletes the gbrain home and only offers --delete-brain for a
brain it created; read-only PGLite lock probe (never opens the engine).
54 unit tests, injectable exec seam throughout.

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

* feat(release): latest-stable ref, template-repo publish job, bootstrap CI guards

release.yml advances the latest-stable tag only after assets publish (the paste
block's permanent ref — copies in the wild never rot) and gains a PAT-gated
publish-template job verified against the vendored tree; two skip-graceful
guards (sanctioned-ref + runbook stamp; template/token bijection + placeholder
assertion + generator byte-diff) wired into verify; README + runbook re-admitted
to the CI cache hash; vendored deterministic template tree generated.

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

* feat(context): IPC v2 turn_context + 8KB assembly + visibility resolver + session identity

Discriminated-union IPC with handler map, protocol echo (stale-serve detection),
shared-secret gate, server-side source binding, per-kind budgets; turn-context
assembly (reflex pointers + volunteered pages + world-only hot facts) under a
data-not-instructions envelope trimmed to the harness's 10KB hook-output cap;
facts.default_visibility resolved through one helper at all four sites (explicit
caller wins, typos fail closed); typed sessionId threads _meta.session_id into
the hot-memory cache key. 50 new tests; 180 adjacent tests confirmed green.

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

* feat(persistence): secret-scan, gbrain sources push, durability unification

Pattern secret scanner (own runtime allowlist, redacted previews, corpus-write
redaction mode); sources push runs the whole scan→stage→commit→pull→push
sequence under one cross-platform lock (mkdir-atomic, pid+age+token) with a
deny-glob backstop, commit-first divergence-safe pull, refuse-unverifiable
visibility, and push-status telemetry; gbrain-home choke point unifies
GBRAIN_HOME semantics with config (0700); durability is parent-repo-aware and
rotates its push log at 0600. 35 new tests; 200 existing green.

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

* fix(sources): harden/pull gates accept sources inside a parent git repo

The bootstrap workspace registers brain/ (a subdirectory) as the source; the
durability core already resolves the repo root, so the command gates now check
inside-a-repo rather than .git-right-here [CX2-3].

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

* feat(serve): resident maintenance sweep + keyless capability probe

The lock-owning serve process now closes the persistence loop: startup (3s
post-connect, best-effort, unref'd) and idle (10-min quiet intervals through
the injectable timer seam) sweeps run facts-fence reconciliation, deterministic
link/timeline extraction over recent workspace pages, and spend-gated corpus
ingest (skipped keyless — agent-authored fences cover it). gbrain sweep --once
is the trusted CLI seam bootstrap verify uses. Capability probe renders the
honest keyless/keyed report. Full reuse of the cycle extractor + extract cores;
26 new tests, neighbors green.

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

* feat(hooks): engine-free gbrain hook command, settings writers, transcript parser

Four hook events (session-start digest + crashed-session recovery push,
user-prompt turn-context injection under an 800ms deadline and the 10KB cap,
stop buffers, session-end corpus write with redaction/retention/dedup +
best-effort push); structural JSON settings merger keyed by a _gbrain marker
(foreign hooks and permissions survive); dated host-spec registry; Claude Code
.jsonl parser as a spec-target with a scrubbed 7-shape fixture. Heartbeat is
counters-only by construction. 59 tests; zero engine modules in the import
graph.

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

* docs(bootstrap): cross-link the full-agent path from the connection docs

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

* feat(bootstrap): dispatcher, verify, status — the command assembled

gbrain bootstrap {status,interview,render,repo,hooks,verify,uninstall,attach}:
engine-free except verify (owns its engine, in-process sweep — no live-serve
conflict); phase list is the TS source of truth with install.jsonl telemetry
and the support blob; verify's fail-soft check suite covers the real write path
(put_page → write-through file → sweep → graph floor → recall), passes keyless,
persists snapshots, and ends with the first-run tour. cli.ts wired per the
three-touchpoint rule; doctor gains the bootstrap check group (silent on
machines with no bootstrap state). 28 new tests; 353 adjacent green.

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

* docs: KEY_FILES bootstrap cluster + CLAUDE.md dispatcher row (+ build:llms)

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

* test(bootstrap): e2e pins — hook-under-live-serve, attach, degraded modes, compiled binary, Docker harness

The permanent pins: a real serve holds the PGLite lock while the engine-free
hook completes (and a direct engine open provably throws LiveServeLockError);
stale-socket fail-open; machine-2 attach with marker-keyed hook repair;
decline-everything installs verify green with every degradation named; the
compiled binary renders bundled templates in an empty cwd. Offline Docker
harness (networkless, read-only) gated into heavy-tests.

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

* fix(bootstrap): register doctor check categories + system-of-record allow comments

The six bootstrap doctor checks join OPS_CHECK_NAMES; the sweep's batch link/
timeline inserts carry the explicit extract-path allow comments (the sweep IS
the extraction path for workspace pages).

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

* fix(test): shard wedge cap tracks suite growth (1500s -> 1800s)

At ~9000 tests a healthy shard finished at 1466s and two progressing shards
were false-killed at the old cap; 1800s restores ~25% headroom over the
slowest observed healthy shard. Real hangs still hit it.

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

* test(ci): cache-hash policy — README + runbook edits must invalidate [C2]

The old deny-list assertion predates the paste block; README.md and
BOOTSTRAP_FOR_AGENTS.md are policy-doc re-admissions now, so their edits must
change the hash (a paste-block edit shipping under a cached green was the C2
hole).

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

* fix(test): classify post-suite exit-hangs as warn-pass; file the leak forensics

A shard killed by the wedge watchdog with every assigned file started and zero
fail markers did all its work and leaked a handle at exit — pre-existing and
master-reproducible (P1 TODO carries the full bisect forensics). Bun's per-test
timeout turns a hung test into a (fail), so the classifier cannot mask one.

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

* fix(test): shard cap 2400s — the count-balanced heavy shard needs it under contention

Observed: the heavy shard still progressing 22s before an 1800s kill while
siblings finish at 1150-1550s (split balances file count, not weight). Filed
the load-sensitive WAL-repair flake (pre-existing, master's v0.42.75.0 wave).

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

* test(bootstrap): quarantine env-mutating suites to the serial lane

check-test-isolation R1: six new files mutate GBRAIN_HOME/env at module scope —
the serial lane (one process per file) is the guard's prescribed home for them.
All 114 tests pass post-rename.

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

* docs(readme): per-harness install sections — Codex, Claude Code, then OpenClaw/Hermes

Each harness gets its own complete paste-block section (desktop app first,
terminal noted — Claude Code CLI is the identical harness; Codex CLI works
pull-based today); the OpenClaw/Hermes platform path keeps equal weight with
its one-click deploys and INSTALL_FOR_AGENTS block intact; memory-only and
remote-connect tiers consolidated under 'Lighter ways in'. Supersedes the
review's D5 ordering by user direction; stale heading references updated.

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

* docs(readme): Codex as the recommended first step; OpenClaw/Hermes framed as-intended, high-cost

The install section now routes newcomers explicitly: Codex first
(subscription-priced, nothing to deploy), OpenClaw/Hermes as GBrain used the
way it was designed — always on, at real server + API cost.

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

* fix: doc-audit code chasers — broken recovery hints, stale op description, auto_link key

Four small code fixes surfaced by the markdown accuracy audit:
- doctor's auto-RLS recovery hint pointed at `apply-migrations --force-retry 35`,
  which cannot work (--force-retry targets the vX.Y.Z orchestrator registry, not
  the numeric schema MIGRATIONS array). Hint now points at the recreate SQL in
  docs/guides/rls-and-you.md; test pins against regression.
- v0_11_0 migration printed the same broken-mechanism class of hint
  (`config set minion_mode` writes DB config nothing reads); now names
  `apply-migrations --mode` + preferences.json, the real setter.
- submit_job's op description hardcoded a stale handler list; now points at
  registerBuiltinHandlers as the source plus the --follow discovery trick.
- `auto_link` added to KNOWN_CONFIG_KEYS: read by link-extraction, reconcile-links,
  and sweep, and documented as the off-switch in brain-ops/maintain, but the
  allowlist rejected `config set auto_link false`.

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

* docs: repo-wide accuracy + MECE reform from the 9-bucket markdown audit

A code-grounded audit of every markdown file (root, architecture, guides,
mcp, tutorials, docs-root, operations/eval/designs, skills, recipes) followed
by a fix wave with per-bucket ownership. Four classes of change:

Accuracy — every documented command/flag verified against src/ before writing:
dead commands replaced with working ones (pages purge-deleted, jobs watch
--follow, gbrain restore, import-based Obsidian flow, space-separated --scopes,
real thin-client recipes, working isolation verification, real supervisor
restart procedure, curl-based ngrok health check, real minion_mode setter);
count drift fixed with rot-proof phrasing (100+ ops, 50+ bundled skills via
skills/manifest.json, 140+ engine methods, KNOBS_HASH_VERSION pointer instead
of hardcoded versions); stale claims corrected (search-mode defaults, RETRIEVAL
pipeline order incl. autocut, sentinel rules, refusal-list mechanism, engine
snapshot, shard cap 2400s + EXIT-HANG classifier in TESTING.md, latest-stable +
publish-template documented in RELEASING.md as release.yml promises).

MECE — one home per concept, pointers elsewhere: test isolation → TESTING.md;
OAuth registration + --bind/--public-url lore → DEPLOY.md; mode bundles →
guides/search-modes.md (the home the CLAUDE.md dispatcher always promised);
merge contract → schema-packs.md; WAL ladder → ENGINES.md; quiet-hours →
quiet-hours.md; capture taxonomy → entity-detection.md; person-page taxonomy →
compiled-truth.md; brain-first protocol → brain-first-lookup.md; refresh
semantics → refresh-algorithm.md; KEY_FILES.md deduplicated (58 extension
entries merged, one entry per file); infra-layer.md rewritten as a pointer page.

Privacy — placeholder sweep across guides, docs, skills, and recipes per the
iron rule; per-release narration stripped from reference docs (current-state
prose only).

Bootstrap coverage — AGENTS.md pointer, RESOLVER routing row, INSTALL.md path,
tutorial cross-links, keyless-mode sections in spend-controls/headless-install.

skills.lock.json regenerated; llms.txt/llms-full.txt rebuilt. Gates: verify
36/36, typecheck clean, doctor 96/96, skills-integrity + resolver + build-llms
+ config-set + migrations all green.

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

* docs(readme): refresh production-brain stats to current brain-repo counts

155,795 pages / 24,589 people / 5,340 companies, counted from the brain
repo's current HEAD; the "100K-page brain" framing moves to 150K to match.
Cron-fleet count unchanged (its store lives on the deployment host, not in
the repos available for verification).

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

* fix(scan,push): modern OpenAI/Voyage key patterns, scan staged blobs not disk

- secret-scan matches sk-proj-/sk-svcacct-/sk-None- and pa- Voyage keys
  (the bare sk- pattern missed every current OpenAI key format).
- workspacePush stages first, then scans the staged index blobs via
  git cat-file, closing the scan-then-stage TOCTOU where a file changed
  between snapshot and commit shipped unscanned.
- shared binary-sniff helper, memoized glob regexes, atomic push-status
  write, and tests for pull_conflict + gitignored deny-match paths.

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

* fix(ci): regenerate flag registry for new commands, harden shard classifier + release token

- cli-flag-registry.generated.ts regenerated: bootstrap/hook/sweep and
  sources push --message/--allow-unverified-remote were missing, so the
  strict #2185 validator rejected real invocations and skipped the new
  commands entirely.
- EXIT-HANG shard classifier now requires every assigned file to have
  started before warn-passing a watchdog kill (was fail-open).
- release.yml passes TEMPLATE_REPO_PAT via http.extraheader, off the argv.
- compiled-binary e2e fails loud in CI instead of a silent permanent skip.

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

* fix(hook,sweep,ipc): non-blocking hook pushes, bounded sweep + cache, source-bound resolve

- session-start/session-end no longer run synchronous git + inline push
  inside their self-deadline; a detached child does the push and the hook
  returns immediately (blocked Claude Code startup for minutes on a dirty
  tree before).
- serve sweep drops the unbounded listAllPageRefs, resolves only candidate
  targets, claims corpus files atomically (no double-LLM-spend race), and
  caps the fence LIKE scan; heartbeat writes are O_APPEND with rare compaction.
- hot-memory cache evicts expired entries and bounds entry count (the key is
  caller-controlled via _meta.session_id).
- v1 resolve IPC honors boundSourceId like turn_context; turn-context runs
  its arms concurrently. doctor reads push/heartbeat thresholds from hook.ts.
- new tests: doctor bootstrap checks, hook push-gate + deadline, concurrent
  sweep claims, cache eviction, bound-source resolve.

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

* fix(bootstrap): origin-ownership gate, world visibility, collision-safe source id, consent + templates

- repo adoption requires an exact receipt repo_url match or authed-owner
  check (undefined repo_url was a wildcard); create verifies privacy BEFORE
  the first push.
- verify sets facts.default_visibility=world if unset, so agent-authored
  facts surface in per-turn context (they defaulted private before).
- source_id derives a path-hash suffix when 'workspace' is taken by another
  checkout; every consumer reads manifest.source_id.
- skipped HOOKS_CONSENT now declines (was falling through to default yes);
  --minimal refuses on an initialized manifest; tilde fences escaped.
- MCP registration pins --surface full; status hard-fails a public origin
  (template door); receipt writers guard against newer/corrupt receipts;
  uninstall only claims brain-deleted after a real rm.
- templates ship jobs disabled + provider-consent + support-relay lines;
  soul-audit re-runs over the shared interview bank. TODOS: 11 follow-ups.

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

* fix(security): close adversarial-review findings — scan fails closed, whole-PEM redaction, bound repo push

Cross-model adversarial pass (Claude + Codex) on the bootstrap wave:

- secret scan fails CLOSED: an unreadable, oversized, or binary staged blob
  now blocks the push (blocked_unscannable, exit 5) instead of committing
  unscanned; only a confirmed staged deletion is skipped. This was the
  headline "block secrets before they leave the machine" property failing open.
- private-key redaction spans the whole PEM block (header+body+footer), not
  just the header line — the base64 body no longer survives into the corpus
  the sweep sends to an extraction provider.
- bootstrap repo commits the workspace (secret-scan-gated) before the first
  push and verifies the remote actually received it, so a push-fail retry
  can't adopt an empty remote as success.
- privacy verify is re-bound to origin immediately before push (a concurrent
  origin rewrite between verify and push is refused).
- session-end corpus write is atomic and clears the stale ingested/in-progress
  sidecars so a resumed session's appended transcript is re-ingested.
- public-origin refusal enforced at render (not only status); MCP "already
  registered" is verified to target this workspace, not blessed blindly;
  verify probe cleanup scopes deletes to its own slugs, not a token substring;
  allowlist fingerprint floor raised 8→16 hex.

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

* v0.45.0.0 feat(bootstrap): paste-in personal-agent install for Codex + Claude Code

Turns a Codex or Claude Code session into a persistent personal agent:
interview-rendered identity files, a local PGLite brain, per-turn context via
serve IPC (Claude Code hooks / Codex pull protocol), session-triggered
persistence, and a private GitHub repo as the agent's portable body. Keyless-
first (the harness model is the LLM; one optional key adds embeddings +
extraction). New `gbrain bootstrap` command family + `gbrain hook` + `gbrain
sweep`; doctor bootstrap health checks; latest-stable distribution ref +
template-repo publish job. Opt-in, additive — existing installs untouched.

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

* fix: regenerate flag registry for security-fix flags; drop fabricated gbrain capabilities doc ref

CI caught two real failures under the merged state:
- the flag registry lagged the blocked_unscannable/exit-5 flags the security
  round added, tripping the #2185 freshness guard.
- headless-install.md described the keyless capability report as a
  `gbrain capabilities` command, which the #3502 doc-command resolver
  rejects — reworded to prose (the real surface is bootstrap verify's report).

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

* docs: sync KEY_FILES + bootstrap plan to security-fix behavior

Cross-referenced the security-fix round against the reference docs and
corrected the drift those commits introduced:

- workspace-push.ts entry: stage-FIRST-then-scan order (the TOCTOU fix),
  fail-closed blocked_unscannable, and the sources-push status -> exit-code map.
- hooks.ts entry: MCP registration pins `serve --surface full`.
- hook.ts entry: session-start/session-end pushes run in a detached child
  (non-blocking); atomic corpus write clears stale sidecars.
- bootstrap.ts entry: render hard-refuses a public origin (template door).
- verify.ts entry: source_id collision resolution (workspace-<path-hash>).
- AGENT_BOOTSTRAP_PLAN as-shipped delta note for the scan/stage reorder.

llms bundle unchanged (KEY_FILES is link-only); build:llms and
test/build-llms.test.ts green.

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

* fix(ci): silence SC2016 on the intentional askpass literal in release.yml

The one-shot GIT_ASKPASS script must contain literal $1 and
$TEMPLATE_REPO_PAT so they expand when /bin/sh runs it at git's credential
prompt, not when the outer shell writes the file — single quotes are correct.
Add a scoped shellcheck disable so actionlint passes.

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

* fix(skills): declare 'bootstrap my data' trigger in cold-start frontmatter

The doc reform added 'bootstrap my data' to cold-start's RESOLVER.md row (to
disambiguate data-bootstrap from agent-bootstrap) but not to the skill's own
frontmatter triggers, tripping the RESOLVER↔frontmatter round-trip contract
(resolver.test.ts). Declare it; regenerate skills.lock.json.

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

* feat(bootstrap): default per-turn hooks + search mode ON without a prompt

Installing gbrain for your coding agent IS the consent for the behaviors that
make it work, so stop re-litigating them with install-time questions whose
"no" defeats the product:

- Per-turn hooks (Claude Code) install ON by default — no prompt. Off-ramps:
  `--no-hooks` at install, `GBRAIN_HOOKS=0` at runtime, `bootstrap uninstall`.
  The "hooks installed" line now surfaces the kill switch so default-on is
  never silent. A persisted HOOKS_CONSENT=no (interview --skip) still declines.
- Search mode defaults to `balanced` silently (nobody knows the modes at
  install; `gbrain search modes` changes it any time).
- MCP scope stays the ONE deliberate prompt — project vs user is a real
  cross-repo privacy choice, not friction.

Marks the two consents `silent: true` in the question bank (new QuestionSpec
field), rewrites the runbook phases so the agent no longer asks them, adds the
`--no-hooks` flag (+ registry regen), and adds default-on / opt-out tests.

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

* test(bootstrap): real end-to-end coverage — cross-session recall, per-turn content, Codex door, realistic corpus

Closes the seven e2e gaps a coverage audit surfaced: the plumbing was
well-unit-tested but the product claims ("Codex works, context shows up every
turn with real content, it remembers across restarts, machine two recovers,
Postgres works") were unproven end to end. Test-only wave — zero src changes.

- Hermetic synthetic corpus (test/fixtures/bootstrap-corpus/ + a loader helper):
  12 interlinked pages (52 edges, timelines), 12 world/private beliefs, 8 gold
  queries — curated from the gbrain-evals synthetic corpora, 100% placeholder
  names, so recall is asserted on a real multi-entity brain instead of a
  2-node self-planted probe.
- GAP1 magic moment: author a fact via the real write path, disconnect the
  engine, reopen against the same DB, recall it — a real session boundary, not
  verify.ts's same-connection SQL read-back. Plus a source-isolation assertion.
- GAP2 per-turn content: hook-under-serve Pin 1 now seeds a known fact and
  asserts its text lands in the injected block AND private beliefs never do
  (was: empty brain, empty_block accepted as a pass).
- GAP3 Codex door: assert the rendered AGENTS.md carries the Gate-3 brain-first
  pull protocol; make the fake codex shim implement `mcp get` so the [FIX7]
  target-verification can actually fail; the Docker cold-machine harness now
  exercises the hooks/MCP registration step instead of skipping it.
- GAP4 corpus recall: turn-context + verify graph-floor/qrels run on the real
  multi-entity brain with real edges.
- GAP5 attach: machine-two now re-ingests the cloned brain/ into a fresh DB and
  recalls a fact authored only on machine one — the multi-device payoff.
- GAP6 keyed + Postgres (env-gated): real embeddings prove semantic recall a
  paraphrase query can reach but keyless BM25 cannot; bootstrap verify drives a
  real Postgres engine (skipIf DATABASE_URL/keys absent).
- GAP7 persistence: session-end runs the REAL push (not the mocked seam) to a
  local bare remote and the remote receives the content; a planted secret is
  blocked at the gate; the 15-min cron installs and fires a scan-gated push.

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

* test(bootstrap): real-agent e2e — drive the actual claude + codex binaries end to end

Closes the audit's biggest gap ("no real harness ever drives a turn"). Adapts
gstack's PTY/headless agent harness to prove the bootstrap install + smoke work
against the REAL binaries, not PATH shims. Test/CI/docs only — zero src changes.

- test/helpers/agent-harness.ts: hermetic clean-room child env (ported from
  gstack; drops CONDUCTOR_/CLAUDE_/GSTACK_/MCP_/GBRAIN_, promotes
  GSTACK_ANTHROPIC_API_KEY→ANTHROPIC_API_KEY), real-binary resolvers + auth
  probes, headless `claude -p --output-format stream-json` and `codex exec
  --json` turn runners, a gbrain stdio MCP-config writer, and a keyless brain
  seeder. + a fixture-parse unit test (no binary needed).
- test/e2e/bootstrap-real-claude.serial.test.ts: real `gbrain bootstrap`
  install → REAL `claude mcp add` (verified via `claude mcp get`) → verify
  exit 0 → a real `claude -p --mcp-config --strict-mcp-config` turn that
  invokes mcp__gbrain__search and answers from the brain (proven: toolCalls
  include mcp__gbrain__search, final text carries the seeded fact).
- test/e2e/bootstrap-real-codex.serial.test.ts: same install with REAL `codex
  mcp add` into a real ~/.codex/config.toml + Gate-3 pull-protocol assertion,
  then a real `codex exec --json` turn surfacing the fact (MCP or the pull-
  protocol shell path). Bounded retry absorbs codex's occasional MCP-call
  cancellation without softening the fact-requiring assertion.
- Everything hermetic (temp HOME/CLAUDE_CONFIG_DIR/CODEX_HOME/GBRAIN_HOME;
  real ~/.codex auth copied read-only) and skipIf-gated so it self-skips
  cleanly where the binaries/auth are absent.
- heavy-tests.yml: gated `real-agent-e2e` job (nightly/label, never the PR
  shard; no-op on a runner without authed binaries).
- TODOS: compiled `gbrain` binary can't serve a PGLite brain (bun compile
  omits the WASM/extension payloads); harness falls back to `bun run` serve.

Verified against live claude 4.6 + codex 0.147.0: 15 pass / 0 fail; verify
36/36; typecheck clean.

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

* fix(ci): real-agent-e2e job — bash array + --timeout (actionlint SC2086 + bun-test-timeout guard)

The real-agent-e2e job's file loop used an unquoted $FILES (SC2086) and ran
`bun test` without --timeout (check-bun-test-timeout guard). Switch to a bash
array and add --timeout=600000 (real-agent turns are slow; the tests self-skip
without authed binaries so it's a no-op elsewhere).

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

* fix(pglite): embed WASM + extension assets so the compiled binary can serve

A `bun build --compile` gbrain binary could not `serve` a PGLite brain: the
compile bundles JS but not PGLite's runtime payload (pglite.wasm, initdb.wasm,
pglite.data, vector/pg_trgm tarballs), so `serve` on PGLite died with a
bunfs/ENOENT. Now the assets ride inside the binary.

- src/core/pglite-embedded-assets.ts: embeds the five assets via
  `import … with { type: 'file' }` (the ENG-6 idiom) and exposes
  getEmbeddedPgliteOptions() → { pgliteWasmModule, initdbWasmModule, fsBundle,
  extensions:{vector,pg_trgm} }. WASM/fsBundle are consumed as bytes; the two
  extension tarballs are materialized to a content-addressed temp file (atomic,
  size-verified reuse) because PGLite reads them via fs.createReadStream, which
  cannot read a /$bunfs path. Unconditional (works in bun-run and compiled),
  so no fragile mode branch.
- src/core/pglite-engine.ts: static-import getEmbeddedPgliteOptions (engine
  path stays static per the engine-dynamic-import invariant); spread into both
  PGlite.create sites (initial + WAL-repair retry). The bunfs classifier stays
  as a backstop but no longer fires for a correct binary.
- scripts/check-pglite-embedded.sh (+ smoketest): compiles a focused binary and
  asserts it boots PGLite, CREATE EXTENSION vector/pg_trgm, and round-trips a
  page — wired into `bun run verify` (now 37 checks), check:all, and
  check:pglite-embedded. Fail-soft only when compile is unavailable.
- agent-harness.ts probeCompiledPglite now passes → the real-agent e2e uses the
  fast compiled MCP server. TODOS: the P2 "can't serve PGLite" item is closed.

Verified: fresh compiled binary ran `search`/`query` against a PGLite brain and
returned the seeded row (no bunfs/ENOENT); verify 37/37; pglite-engine 120/0
source-mode; typecheck clean; engine-dynamic-import + parity guards pass.

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

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
 2026-08-11 16:42:11 -07:00
Time AttakcClaude Fable 5Garry Tan
 		0bbaed2e48 v0.42.67.0 feat(migrate): provider-agnostic embedding migration — the path off ZeroEntropy (#3390, fixes #3391) (#3459) 
* feat(migrate): provider-agnostic embedding migration service — the path off ZeroEntropy (#3390)

- gbrain migrate embeddings --to <provider:model> (alias: retrieval-upgrade):
  plan + cost preflight, consent gate (--yes / TTY confirm / non-TTY exit 2),
  live probe against the target provider before any mutation, env-override
  gate, schema dimension transition via the shared runSchemaTransition,
  dual-plane config write, NULL-signature-inclusive invalidation, query-cache
  purge, resumable re-embed through the standard embed pipeline (single-flight
  locks, backoff, pacing, stderr progress). Killed runs resume by re-running
  the same command; the NULL-embedding column is the checkpoint.
- #3391 root-cause fix (both engines): countStaleChunks / sumStaleChunkChars /
  invalidateStaleSignatureEmbeddings accept includeNullSignature to lift the
  v108 grandfather clause; embed --stale warns loudly when a model swap
  leaves NULL-signature pages in the old embedding space, and
  --include-null-signature re-embeds them. Default sweep behavior unchanged.
- knobs_hash v=12 → v=13 (prov=default legacy callers must not be served
  pre-migration cache rows).
- migrate_embeddings op: scope admin, localOnly, hidden cliHints, hard
  remote refusal, needs_confirmation without yes=true.
- One-shot post-upgrade ZE-sunset banner (ze_sunset_notice_shown) for brains
  resolving to a zeroentropyai:* embedding model or reranker.
- doctor's dimension-mismatch repair hint now names the real command.
- Docs: docs/guides/embedding-migration.md, KEY_FILES entries, spend-controls
  gate row. Tests: PGLite unit + full-lifecycle flow (interrupted-run resume),
  real-Postgres e2e (pgvector DDL path + #3391 predicate parity).

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

* fix(test): satisfy check:test-isolation + bump the remaining knobs_hash pins

- test/migrate-embeddings-flow.test.ts → .serial.test.ts: the file holds a
  temp GBRAIN_HOME + an installed fake embed transport for its whole
  lifecycle (beforeAll → afterAll), which withEnv() can't wrap. This also
  fixes the CI shard-pollution failure in
  test/ai/recipes-existing-regression.test.ts (that file passes solo on both
  master and this branch; the flow test's configureGateway + provider-key
  deletion was leaking into it inside the same shard process).
- test/embedding-migration.test.ts: env-override case now uses withEnv().
- Bump the three remaining KNOBS_HASH_VERSION pins to 13
  (cross-modal-phase1, search-alias-resolved-boost, search/knobs-hash-reranker).
- Docs + llms bundles follow the test rename.

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

* chore(test): wire the new Postgres e2e into the smart e2e selector map

Changes to embed.ts / embedding-migration.ts / retrieval-upgrade-planner.ts /
postgres-engine.ts now trigger test/e2e/migrate-embeddings-postgres.test.ts —
the #3391 stale predicates and runSchemaTransition's DDL path behave
differently on real pgvector than on PGLite, so the smart selector has to know.

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

* feat(migrate): consult spend.posture in the embedding-migration consent gate

The brief asked the gate to honor spend.posture; it previously didn't read it
at all. Now it does — but deliberately does NOT bypass on tokenmax: posture
waives the spend CEILING, and this gate also guards a destructive schema
rebuild (existing vectors dropped, retrieval degraded until the re-embed
finishes). Under tokenmax the dollar figure is marked informational on stderr
and the confirmation is still asked; --yes stays the single scripted bypass.

Pinned by a new case in the flow test so a later refactor can't quietly turn
posture into a bypass. Guide + spend-controls table updated to match.

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

* wip: blocker fixes

---------

Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
 2026-07-27 17:48:37 -07:00
Time AttakcClaude Fable 5Garry TanFloridaStyle
 		32d42454e9 v0.42.66.0 fix(extract): make conversation backfill outcomes durable (takeover of #3293) (#3373) 
* v0.42.66.0 fix(extract): make conversation backfill outcomes durable (takeover of #3293)

Versioned, snapshot-bound terminal audit rows become the durable authority
for conversation fact backfill completion; checkpoint GC can no longer
repeat completed model work, and best-effort empty results no longer mask
provider/output failures as complete.

Supersedes #3293 (rebased onto current master; only version-trio conflicts).

Co-authored-by: FloridaStyle <danwiggins@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore: drop version-trio bump — individual fixes do not carry version bumps (release PRs do)

* merge: reconcile durable-outcome skip accounting with master's LLM fallback tests

The two fallback replay tests from #3371 asserted the legacy checkpoint
pages_skipped counter; under this PR's durable-outcome authority a
completed page is skipped via pages_skipped_completed before any parse.

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

---------

Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: FloridaStyle <danwiggins@users.noreply.github.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
 2026-07-24 12:27:56 -07:00
Time AttakcFloridaStyleClaude Fable 5Garry Tan
 		f64505b75f v0.42.66.0 feat(conversation-parser): wire the opt-in LLM fallback (#2247) (#3371) 
* v0.42.66.0 feat(conversation-parser): wire the opt-in LLM fallback (#2247) (takeover of #3292)

Rebase of PR #3292 onto current master (version trio re-resolved to
0.42.66.0; code applied cleanly). Wires the existing conversation-parser
LLM fallback into conversation fact extraction behind the exact,
default-off conversation_parser.llm_fallback_enabled=true privacy gate.
Deterministic parsing stays first; dry runs never call a provider.

Co-authored-by: FloridaStyle <daniel.wiggins@gmail.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* chore: drop version-trio bump — individual fixes do not carry version bumps (release PRs do)

---------

Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: FloridaStyle <daniel.wiggins@gmail.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
 2026-07-24 11:36:01 -07:00
Garry TanandClaude Opus 4.8 5c49225e4b v0.42.45.0 feat(sync): delta-aware cost estimator — stop wedging the daily cron (#2139) (#2224) 
* feat(core): shared computeSyncDelta + spend-posture module (#2139)

sync-delta.ts: ONE implementation of "what changed since last_commit",
consumed by both the sync executor and the inline cost estimator so the
gate's dollar figure can't drift from what the sync imports.

spend-posture.ts: spend.posture config + parseUsdLimit/formatUsdLimit
off-switch parsing (off/unlimited/none → Infinity; undefined at the budget
boundary so ledger rows never serialize null).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* feat(sync): delta-aware cost estimator + non-TTY auto-defer + per-source failure acks (#2139)

The inline-embed cost gate was a ~400x phantom: it priced the entire tree
whenever the working tree was dirty (always, on an active brain), then blocked
the daily cron with exit 2. Now:

- performSyncInner + the estimator both route through computeSyncDelta, so the
  estimate mirrors execution (fetch-first delta; dirty-but-caught-up tree → $0).
- shouldBlockSync is posture-aware; non-TTY above floor AUTO-DEFERS embeds to
  capped backfill jobs (exit 0) instead of wedging — single shared
  runInlineCostGate on both --all and single-source paths.
- --full prices delta + stale backlog (full sync sweeps it inline).
- off/unlimited on the cost knobs; tokenmax bypasses the backfill cap (still
  ledgered) but never the cooldown.
- --skip-failed/--retry-failed scoped per source; the D15 parallel refusal is
  lifted (the #1939 ledger is per-source + lock-serialized).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* feat(config): register spend-control keys + validate spend.posture (#2139)

Adds spend.posture + the five previously --force-only spend knobs to
KNOWN_CONFIG_KEYS so `config set` accepts them directly (removes the
archaeology the issue complained about), and rejects invalid spend.posture
values at set time with a paste-ready hint.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* feat(reindex,enrich,onboard): spend.posture across the remaining cost gates (#2139)

reindex-code: tokenmax makes the cost gate informational; --max-cost accepts
off/unlimited. enrich + onboard --auto: tokenmax lifts the refuse-without-cap
guardrail and runs UNCAPPED (spend still ledgered by BudgetTracker). Explicit
--max-usd always wins over posture.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* test: cost-gate, delta estimator, spend-posture, off-switch coverage (#2139)

New sync-delta + sync-cost-estimate unit suites; rewritten cost-gate serial
tests (auto-defer instead of exit 2, posture, off-switch, format split,
single-source); parseUsdLimit/posture-aware shouldBlockSync; backfill cap-off
+ tokenmax-bypass + cooldown-still-refuses; config known-key acceptance.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs(spend-controls): single spend-control surface + ref-map + follow-up TODOs (#2139)

New docs/operations/spend-controls.md (every gate, key, default, off switch,
posture interaction); CLAUDE.md reference-map row; two P3 follow-up TODOs
(measured chunk-count gating, per-source defer granularity). llms bundles
regenerated.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* fix(spend): SSRF-harden estimator fetch + complete off/uncapped across reindex/enrich/onboard (#2139)

Ship-stage codex pre-landing review caught four P1s in the secondary cost gates:

- The delta estimator's fetch-first ran `git fetch` through the plain git()
  helper, bypassing the GIT_SSRF_FLAGS + GIT_TERMINAL_PROMPT=0 hardening that
  real sync uses. Added `fetchRemote()` to git-remote.ts (same flags as
  pullRepo) and route the estimator through it — a cost preview / dry-run can
  no longer hit a remote through a less-protected path.
- `reindex --max-cost off`, `enrich --max-usd off`, `onboard --auto --max-usd
  off` were parsed but didn't actually proceed/uncap. Now: explicit off (and
  spend.posture=tokenmax) proceed past the confirmation/missing-cap refusal AND
  run uncapped. enrich threads an Infinity sentinel mapped to "no BudgetTracker
  ceiling" (never raw Infinity → no null in audit rows); reindex/onboard use
  their native undefined=uncapped path. Spend still ledgered.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* chore: bump version and changelog (v0.42.45.0)

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* docs(KEY_FILES): update sync/embedding/git-remote/reindex entries to post-#2139 truth

document-release pass: the cost-gate entries described the pre-#2139 behavior
(full-tree-ceiling estimator, --skip-failed-rejects-under-parallel, exit-2
confirmation gate). Updated to current truth — delta-aware estimator via the
shared computeSyncDelta, per-source failure acks under parallel, non-TTY
auto-defer (no exit 2), posture-aware shouldBlockSync. Added entries for the
two new core modules (sync-delta.ts, spend-posture.ts) + fetchRemote on
git-remote.ts + reindex --max-cost off.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
 2026-06-16 15:08:47 -07:00
Garry TanandClaude Opus 4.7 a55de71221 v0.37.10.0 feat(init): env-detection + interactive picker + preflight invariants (#1278) 
* feat(core): Levenshtein helper + preflight schema-dim resolvers

Foundation for v0.37.10.0 env-detection wave. Two pure modules:

- src/core/levenshtein.ts: editDistance(a,b) + suggestNearest(input, candidates, maxDistance).
  Used by config-set "did you mean" suggestions and env-var typo detection at init.
- src/core/embedding-dim-check.ts: resolveSchemaEmbeddingDim() +
  resolveSchemaMultimodalDim() pure functions. Validate resolved dim against
  recipe default_dims + per-provider Matryoshka allow-lists (OpenAI text-3,
  Voyage flexible-dim, ZeroEntropy zembed-1) BEFORE any DB write. Plus
  EmbeddingDisabledError + assertEmbeddingEnabled() runtime guard for the
  deferred-setup path (D9). New PGVECTOR_COLUMN_MAX_DIMS=16000 exported.

Tests: 41 unit cases across both modules.

* feat(providers): extract formatRecipeTable + add init provider picker

Two changes prepping the env-detection wave:

- providers.ts: extract formatRecipeTable() helper from runList(). Picker
  reuses it so UI can't drift from \`gbrain providers list\`. Also adds the
  codex finding #10 warn-line to \`providers test\` when the tested model
  differs from the configured default ("Note: tested X in isolation;
  gbrain's configured embedding is Y — this test does NOT verify your
  brain's active path."). envReady() takes an explicit env arg for testing.

- init-provider-picker.ts (NEW): interactive picker mirroring
  init-mode-picker.ts. Filters candidate recipes to env-ready ones
  (codex finding #3), prompts via readLineSafe, exports
  printSubagentAnthropicCaveat() for shared use from initPGLite/initPostgres.

Tests: 17 unit cases (10 providers + 7 picker).

* feat(config): embedding_disabled sentinel + strict unknown-key rejection

Two changes for the v0.37.10.0 wave:

- src/core/config.ts: add embedding_disabled?:boolean to GBrainConfig (D9
  deferred-setup sentinel, mutually exclusive with embedding_model). Export
  KNOWN_CONFIG_KEYS (60+ canonical keys, file-plane + DB-plane) and
  KNOWN_CONFIG_KEY_PREFIXES (search., models., dream., cycle., etc.) for
  validation use.

- src/commands/config.ts: D6 strict-default unknown-key rejection.
  Unknown key + no --force → exit 1 with Levenshtein suggestion against
  KNOWN_CONFIG_KEYS. Prefix matches accepted without --force. --force
  escape hatch accepts arbitrary keys with stderr WARN. Closes the
  silent-no-op class the bug reporter hit (embedding.provider,
  embedding.model, embedding.dimensions all exit 1 with right suggestion).

Tests: 19 unit cases pinning the bug-reporter regression + gate logic.

* feat(init): env-detection auto-pick + preflight + atomic persist + --no-embedding

Core of the v0.37.10.0 wave (D1-D7, D9-D11). Closes the bug where a fresh
\`gbrain init --pglite\` silently produced a broken brain when no provider
key matched the v0.36 default.

resolveAIOptions rewritten with per-touchpoint env detection:
- Explicit flag → shorthand → env auto-pick (group by provider id, codex #2)
- Picker fires when multiple providers env-ready (D1+D2 hybrid)
- Non-TTY zero-key exits 1 with paste-ready setup hint (D3) + Levenshtein
  typo detection for OPENAPI_API_KEY → OPENAI_API_KEY (D13)
- All three touchpoints covered (embedding + expansion + chat, D4)
- Local-only providers (Ollama/llama-server) excluded from auto-pick;
  picking Ollama silently when user has OPENAI_API_KEY set was wrong UX

initPGLite + initPostgres:
- Drop conditional configureGateway gate → always call before initSchema
- Preflight resolveSchemaEmbeddingDim() BEFORE engine.initSchema() (D11) —
  invalid dim refuses with paste-ready hint, no disk write
- Atomic embedding-config persistence (codex #13): either resolved tuple
  or embedding_disabled:true sentinel, never partial state
- Post-initSchema invariant assertion stays as regression guardrail
- --no-embedding opt-in flag (D9) for deferred-setup mode
- Subagent-Anthropic caveat (D7) fires post-init when chat_model is
  non-Anthropic AND ANTHROPIC_API_KEY missing

Exported groupReadyByProvider() + findEnvKeyTypos() for unit testing.

Tests: 21 unit cases covering provider grouping + typo detection edge cases.

* feat(embed,import): refuse cleanly when --no-embedding deferred-setup is active

T7 of the v0.37.10.0 wave. Both runEmbedCore and runImport now call
assertEmbeddingEnabled(loadConfig()) at entry. When the brain was init'd
with --no-embedding (config has embedding_disabled:true), they exit 1
with a paste-ready hint:

  gbrain config set embedding_model <provider>:<model>
  gbrain config set embedding_dimensions <N>
  gbrain init --force --embedding-model <provider>:<model>

\`gbrain import --no-embed\` flag still works (chunks land without vectors),
so users can still ingest in deferred-setup mode and backfill embeddings
later with \`gbrain embed --stale\`.

* feat(doctor): empty-config drift detection + subagent-Anthropic caveat extension

Two doctor check extensions for v0.37.10.0:

T9 — embedding_provider check extended for the v0.36 silent-default
repair case. When config is empty AND schema column dim differs from the
gateway-resolved default, surface the mismatch with empty-brain vs
non-empty-brain repair branching (codex finding #7 nuance):
- Empty brain (0 embedded chunks) → \`gbrain init --force --pglite
  --embedding-model <id> --embedding-dimensions <N>\` (drop and re-init)
- Non-empty brain → \`gbrain retrieval-upgrade --to <id> --reindex\`
Gated on totalChunks > 0 so pristine empty brains aren't pre-warned.
Never recommend rm -rf ~/.gbrain.

T10 — subagent_provider check (v0.31.12) extended per D7. When chat_model
is non-Anthropic AND ANTHROPIC_API_KEY is missing, warn that subagent
features (gbrain dream, gbrain agent run, gbrain autopilot) will fail at
job submission. Chat alone (gbrain think) still works.

* feat(reindex,test): multimodal preflight + E2E suite for fresh PGLite init

T11 — reindex-multimodal.ts: hook resolveSchemaMultimodalDim() preflight
BEFORE the reindex sweep. Mirrors the text-side contract from initPGLite —
if the configured multimodal model can't produce a dim matching the schema
column, fail loud here with a \`gbrain config set\` hint rather than
mid-reindex with a vector(N) INSERT error.

T12 — test/e2e/init-fresh-pglite.test.ts (NEW, 14 cases): subprocess-driven
E2E verification of the bug-reporter's repro scenarios:
- Happy path: OPENAI_API_KEY set → auto-pick OpenAI, persists config
- D3 non-TTY fail-loud (with and without env-key typos)
- D6 regression: bug-reporter's three no-op config keys all exit 1 with
  Levenshtein suggestions
- D9 deferred-setup mode + gbrain import refusal (and --no-embed bypass)
- D11 preflight refuses BEFORE any disk write
- Explicit --embedding-model wins over env detection

Each test uses its own throw-away GBRAIN_HOME for hermetic runs.

* docs: env-detection + headless-install + close v0.32 picker TODO

T13/T14 docs sync for v0.37.10.0:

- docs/integrations/embedding-providers.md: TL;DR table refreshed to reflect
  ZE as v0.36 default; added "Init resolves your provider from env keys"
  section explaining the auto-pick → picker → fail-loud chain; added
  "If first import fails" troubleshooting block pointing at gbrain doctor
  instead of \`rm -rf ~/.gbrain\`.

- docs/operations/headless-install.md (NEW): Docker/CI sequencing guide.
  Two acceptable patterns — provider key at build time (Pattern 1) or
  --no-embedding opt-in + runtime config (Pattern 2). Codex finding #11.

- README.md: Troubleshooting section with one-paragraph repair hint and
  links to embedding-providers.md + headless-install.md.

- TODOS.md: closed v0.32.x "interactive provider chooser" entry as
  SUPERSEDED by this wave. Added four follow-up entries (dedicated v0.36
  broken-install migration, namespaced ext fields, runtime config-key
  audit, value-level Levenshtein on config set).

* chore: bump version and changelog (v0.37.10.0)

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* fix(doctor): empty brain scores 100/100 + hermetic doctor-report-remote test

Two fixes coupled because the test couldn't pass without the formula fix:

src/core/pglite-engine.ts + src/core/postgres-engine.ts — empty brain
(pageCount === 0) now gets FULL marks (100/100), not 0/100. Semantically
an empty brain has no coverage problem to penalize — there's nothing to
embed, nothing to link, nothing to orphan. Vacuous truth applies. The
pre-fix "empty = 0" caused fresh-init brains to score as critically
unhealthy on \`gbrain doctor\`, which was a structural surprise to users
who'd just run init successfully. Same fix on both engines.

test/brain-score-breakdown.test.ts — updated the "empty brain" assertion
to match the new contract (was: 0/0/0/0/0/0; is: 100/35/25/15/15/10).

test/doctor-report-remote.test.ts → renamed to .serial.test.ts and made
hermetic. The pre-fix test pulled audit data from the host ~/.gbrain
(reranker_health, sync_failures, etc.), which made the assertion
non-deterministic depending on whoever ran the suite. Now isolates
GBRAIN_HOME to a tempdir via beforeAll/afterAll; env mutation requires
serial-quarantine per scripts/check-test-isolation.sh R1.

Closes the master-state flake that was failing on every \`bun run test\`
run regardless of my branch contents.

* docs: update CLAUDE.md and TODOS.md for v0.37.10.0 empty-brain fix

- CLAUDE.md: annotate src/core/pglite-engine.ts + src/core/postgres-engine.ts
  entries with v0.37.10.0 empty-brain 100/100 contract. Vacuous truth: an
  empty brain has no coverage to penalize, so getBrainScore returns full
  marks (35/25/15/15/10 breakdown) when pageCount === 0. Pre-fix 0/100
  was structurally surprising on fresh init and caused the v0.37.8.0
  doctor-report-remote.test.ts flake.
- TODOS.md: mark P0 doctor-report-remote.test.ts:65 TODO completed
  (resolved by commit 9aa571f3's empty-brain-100/100 fix; test renamed
  to .serial.test.ts and made hermetic per scripts/check-test-isolation.sh R1).
- llms-full.txt: regenerated from updated CLAUDE.md per CLAUDE.md "Auto-derived
  files" rule.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* fix(init): D5 persisted-config-wins on re-init + CI mechanical E2E

Two coupled fixes for the v0.37.10.0 wave's interaction with CI's Tier-1
mechanical E2E suite (which runs without any embedding-provider env var).

src/commands/init.ts — Honor D5 properly at resolveAIOptions entry. Pre-fix
the env-detection branch fired on EVERY init regardless of persisted
config. A non-TTY re-init with no env keys exited 1 (D3 fail-loud) even
when ~/.gbrain/config.json already had embedding_model set from a prior
successful init. Now resolveAIOptions reads loadConfig() first and seeds
out.embedding_model / embedding_dimensions / expansion_model / chat_model
from the file plane BEFORE running env detection. Also honors
embedding_disabled (D9 sentinel) on re-init so deferred-setup brains
don't re-trigger fail-loud.

test/e2e/mechanical.test.ts:722 — Setup Journey's first init runs against
a fresh DB with no persisted config. Pass --embedding-model explicitly
(openai:text-embedding-3-large) so the preflight resolves offline. After
this init writes config, subsequent inits in the file (RLS self-heal v24,
RLS event-trigger probes, etc.) honor the persisted config via the D5
fix above.

Verified locally: full test/e2e/mechanical.test.ts → 78 pass / 0 fail.

---------

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
 2026-05-21 18:57:05 -07:00