Files
gbrain/docs/guides/search-modes.md
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

10 KiB

Search Modes

Two decisions shape every gbrain lookup, and this guide covers both:

  1. Which mode bundle your brain runs — conservative / balanced / tokenmax, the named cost-knob presets that control cache, token budget, query expansion, and result count. This is the config-level decision you make once (at gbrain init or via gbrain config set search.mode).
  2. Which lookup verb to use per call — gbrain search (keyword), gbrain query (hybrid), or gbrain get (direct). This is the per-lookup decision an agent makes on every question.

The three mode bundles

A search mode is a named preset that sets every search-cost knob at once. The bundles are frozen in src/core/search/mode.ts (MODE_BUNDLES):

Knob conservative balanced tokenmax
cache.enabled true true true
cache.similarity_threshold 0.92 0.92 0.92
cache.ttl_seconds 3600 3600 3600
intentWeighting true true true
tokenBudget 4000 12000 off
expansion (LLM multi-query) false false true
relationalRetrieval false true true
searchLimit default 10 25 50
  • conservative — smallest payloads. Pairs naturally with a cheap downstream model (Haiku-class) or a high query volume.
  • balanced — the default and the fallback when no mode is set.
  • tokenmax — no token budget, LLM query expansion on, 50 results. Pairs with an expensive downstream model you want fully fed.

Two of the knobs deserve a sentence:

  • expansion rewrites your query into multiple variants via a cheap LLM call per search (adds roughly $1.50 per 1K queries) — better recall, small extra cost.
  • relationalRetrieval adds a graph-walk recall arm for relational questions ("who invested in X", "what connects A and B"); it's a pure no-op for non-relational queries. The query op's relational flag forces it on/off per call.

Setting and resolving the mode

gbrain config set search.mode tokenmax

Per-knob resolution (highest first):

per-call SearchOpts → per-key config override (search.cache.enabled, …) →
  MODE_BUNDLES[search.mode] → MODE_BUNDLES.balanced (fallback)

Mode resolution lives in bare hybridSearch, not just the cached wrapper, so eval replays test the same mode-affected behavior as the production query op. The query cache folds the active knobs into its key (knobs_hash), so switching modes never serves you a stale result set from a different configuration.

Cost intuition

gbrain's own cost is rounding error; what the mode really controls is how many tokens your downstream agent pays to read per query. The corner-to-corner spread is ~25x once you pair mode with downstream model. Rough anchors at 10K queries/month, full payload, no cache savings:

Mode \ Downstream Haiku-class ($1/M in) Sonnet-class ($3/M in) Opus-class ($5/M in)
conservative (~4K tok) $40/mo $120/mo $200/mo
balanced (~10K tok) $100/mo $300/mo $500/mo
tokenmax (~20K tok) $200/mo $600/mo $1,000/mo

Scales linearly with volume. Cache hits cut all numbers ~50%; disciplined prompt caching in the agent loop cuts further. Mismatched pairings waste capacity in both directions — a tokenmax payload overwhelms a cheap model, a conservative payload starves an expensive one. The full methodology and realistic-scale walkthrough live in docs/eval/SEARCH_MODE_METHODOLOGY.md.

CLI surfaces

gbrain search modes              # what is running, with per-knob attribution
gbrain search modes --reset      # clear search.* overrides (mode bundle wins)
gbrain search stats [--days N]   # cache hit rate, intent mix, budget drops
gbrain search tune [--apply]     # data-driven recommendations
gbrain search diagnose "<query>" --target <slug>
                                 # trace where a page surfaces (or fails to)
                                 # across the keyword/vector/alias/hybrid layers

The mode picker runs inside gbrain init (non-TTY auto-selects balanced).

Choosing a lookup verb (search vs query vs get)

Independent of which bundle is active, every individual lookup should use the cheapest verb that answers the question.

on user_asks_about(topic):
    # Decision tree: pick the right lookup verb

    if know_exact_slug(topic):
        # Direct get -- instant, no search overhead
        result = gbrain get <slug>
        # e.g., "Tell me about Alice" -> gbrain get alice-example
        # Returns the FULL page -- compiled truth + timeline

    elif topic.is_exact_name or topic.is_keyword:
        # MODE 1: Cheap-hybrid search -- vector + keyword + RRF, NO LLM
        # expansion. Embeds the query when embeddings are configured; the
        # keyword arm still works day-one without them (keyword-only is
        # also available via the search.mcp_keyword_only opt-out).
        results = gbrain search "{name_or_keyword}"
        # e.g., "Find anything about Series A" -> gbrain search "Series A"
        # Returns CHUNKS, not full pages

        # IMPORTANT: search returns chunks
        # If the chunk confirms relevance, THEN load the full page:
        if chunk.confirms_relevance:
            full_page = gbrain get <slug_from_chunk>

    elif topic.is_semantic_question or topic.is_concept_or_landscape:
        # MODE 2: Full hybrid -- adds multi-query LLM expansion on top of
        # vector + keyword + RRF. Owns concept / landscape / "all-of-X"
        # questions: expansion recovers synonym- and outcome-phrased
        # matches a single embedding misses. Costs one LLM expansion call
        # per query -- worth it for these question shapes.
        results = gbrain query "{natural language question}"
        # e.g., "Who do I know at fintech companies?" -> gbrain query "fintech contacts"
        # e.g., "all the companies doing offshore wind" -> gbrain query "..."
        # Returns ranked chunks via vector + keyword + expansion + RRF

        # Same rule: chunks first, then get full page if needed
        if chunk.confirms_relevance:
            full_page = gbrain get <slug_from_chunk>

# Quick reference:
# | Mode        | Command              | Needs Embeddings | Speed   | Best For                                  |
# |-------------|----------------------|------------------|---------|-------------------------------------------|
# | Cheap-hybrid| gbrain search "term" | Uses if present  | Fastest | Known names, exact tokens                 |
# | Full hybrid | gbrain query "..."   | Yes              | Fast    | Concept / landscape / "all-of-X", synonyms |
# | Direct      | gbrain get <slug>    | No               | Instant | When you know the slug                    |

# Progression over time:
#   Day 1:  search (keyword arm works without embeddings)
#   After first embed: vector arm + full hybrid (query) unlocked
#   Once you know slugs: direct get for speed

# Precedence for conflicting information within a page:
#   1. User's direct statements (always wins)
#   2. Compiled truth sections (synthesized from evidence)
#   3. Timeline entries (raw signal, reverse chronological)
#   4. External sources (web search, APIs)

Tricky Spots

  1. Search returns chunks, not full pages. After gbrain search or gbrain query, you get excerpts. Always run gbrain get <slug> to load the full page when the chunk confirms relevance. Don't answer questions from chunks alone when the full context matters.
  2. Search works without embeddings. On day one before any embedding run, gbrain search still works (the keyword arm carries it; the vector arm joins once embeddings exist). Don't tell the user "search isn't available yet" -- search is always available.
  3. Don't use full hybrid for known names. gbrain query "Alice Example" wastes an LLM expansion call. Use gbrain search "Alice Example" or better yet gbrain get alice-example if you know the slug.
  4. Token budget awareness. A full page via gbrain get can be large. Read the search chunks first to confirm relevance before pulling the full page. "Did anyone mention the Series A?" -- search results (chunks) are probably enough. "Tell me everything about Alice" -- get the full page.
  5. Full hybrid needs embeddings to have been run. If gbrain query returns nothing but gbrain search finds results, the embeddings haven't been generated yet. Run the embedding pipeline first.
  6. A populated gbrain search result set is not proof you found everything. Search runs without query expansion, so synonym- and outcome-phrased matches can be missed even when it returns plenty of hits. For "find every / all / the landscape of" questions, use gbrain query; for literal exhaustive enumeration ("list every page of type X"), use list_pages pagination. A nonzero count is not a completeness signal.

How to Verify

  1. Run gbrain search "Alice" -- confirm it returns chunks with matching text and slug references.
  2. Run gbrain query "who works at fintech companies" -- confirm it returns semantically relevant results (not just keyword matches on "fintech").
  3. Run gbrain get alice-example -- confirm it returns the full page with compiled truth and timeline.
  4. Compare: search for the same entity using all three modes. Keyword should be fastest, hybrid should surface conceptual matches, direct should return the complete page.
  5. After a search returns a chunk, run gbrain get on the slug from that chunk. Confirm the full page contains more context than the chunk alone.
  6. Run gbrain search modes -- confirm the active mode bundle and any per-key overrides are what you expect.

Part of the GBrain Skillpack.