…dential clients (#1253)

* fix(reindex-frontmatter): connect engine before query (#1225)

`createEngine()` from src/core/engine-factory.ts only constructs the
engine; callers MUST call connect() before any executeRaw. The
reindex-frontmatter CLI was constructing the engine and going
straight to countAffected, which crashed on PGLite with "PGLite not
connected. Call connect() first." even on --dry-run.

Fix follows the existing-command pattern (src/commands/auth.ts,
src/commands/backfill.ts, src/commands/integrity.ts all do the
same): pass toEngineConfig(cfg) into both createEngine() AND
engine.connect(), then engine.initSchema() (idempotent on a current
schema, ~1ms cost).

Pre-fix verification: codex outside-voice CF5 flagged the related
"can't import connectEngine from cli.ts" misdirection in the
original fix plan. This implementation uses the canonical sibling
pattern instead.

Regression test pinned at test/reindex-frontmatter-connect.test.ts.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* chore: bump VERSION to 0.37.7.0 + stub CHANGELOG

v0.37.5.0 claimed by #1229 (warsaw-v4); v0.37.6.0 by #1246
(OpenRouter recipe). v0.37.7.0 is the next free slot for this
fix wave.

CHANGELOG entry stubbed in user-facing voice per CLAUDE.md
"CHANGELOG voice + release-summary format" — ELI10 lead-first,
real fix details below. The "## To take advantage of v0.37.7.0"
block follows the v0.13+ self-repair pattern from CLAUDE.md.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(subagent): short-circuit terminal-on-resume (#1151)

Bug: when the worker resumed a subagent job whose persisted last
message was an assistant turn with text-only content (no tool_use
blocks), the replay reconciler at subagent.ts:241-247 had no
branch for that case. The main loop then called messages.create
against a conversation ending in assistant role, which Sonnet 4.6+
rejects with HTTP 400 "This model does not support assistant
message prefill." 3 retries later → dead-letter, despite all the
job's work having committed in earlier turns.

@zscgeek's bug report pinned this exactly: dream-cycle Otter
corpus runs hit ~7% dead-letter rate, every dead job's last
subagent_messages row was a text-only synthesis summary listing
slugs that already existed in `pages`. Their proposed fix mirrors
this implementation.

Fix: add an else branch to the assistant-tail check that mirrors
the live-loop terminal logic at subagent.ts:440-447 — reconstruct
finalText from the persisted text blocks, return
stop_reason='end_turn' immediately. No LLM call, no schema change.

Two new regression cases:
  - text-only terminal on resume returns immediately with zero
    messages.create calls
  - tool-use replay path unchanged (existing behavior preserved)

Codex outside-voice (CF13) initially flagged this fix as
mis-targeted, claiming subagent.ts already handled the case.
/investigate run revealed the live-loop terminal at :440-447 was
covered but the REPLAY-path terminal at :241-247 was missing —
both branches need symmetric handling.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(autopilot): scope lockfile to GBRAIN_HOME (#1226)

The autopilot lockfile was hardcoded at `~/.gbrain/autopilot.lock`
(via `process.env.HOME`), bypassing GBRAIN_HOME. Two brains pointed
at different GBRAIN_HOME directories still wrote to the same global
lockfile; one would silently take over the other on each restart.

Fix: route through `gbrainPath('autopilot.lock')` from
src/core/config.ts (imported aliased as gbrainHomePath since the
local `gbrainPath` var in installAutopilot references the CLI
binary path). The mkdirSync(`~/.gbrain`) call also routes through
the helper so the directory is created in the right place too.

Co-authored with @rafaelreis-r — same fix shape as PR #1227,
re-implemented against current master per the wave's
"re-implement, credit, close" workflow.

Tests cover: one GBRAIN_HOME → one canonical lock; two
GBRAIN_HOME values → two distinct locks; default fall-through
still works.

Co-Authored-By: rafaelreis-r <noreply@github.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(graph-query): foreign-edge footer + --include-foreign (#1153)

The graph-query CLI silently dropped edges to pages in other sources
on federated brains. Users had no signal those edges existed unless
they read the source code.

Fix:
- New --include-foreign flag (off by default, preserves the existing
  scoping contract; on = explicit cross-source traversal).
- After every traversal, count edges from rootSlug whose target page
  lives in a different source. When count > 0 AND user didn't opt in,
  emit a stderr footer:
    `(N edge(s) to foreign-source pages hidden; pass --include-foreign
     to include them)`
- The "no edges found" path also runs the count + footer so users
  discover foreign edges even when scoped traversal returned nothing.
- Thin-client path skips the count (engine query not available);
  future T1 work threads source resolution through MCP for that path.
- Single quotation correctness in count SQL: page_links table is
  `links` (not `page_links`); JOIN both endpoints to pages and compare
  source_id, NULL-safe via `IS NOT NULL` guards on both sides.
- Fail-open on missing source_id column for pre-v0.18 brains: return 0
  (no foreign edges to report) instead of throwing.

4 new test cases: footer fires on scoped query with foreign edge,
--include-foreign suppresses footer, zero-foreign no-footer case,
pluralization regression guard.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(sources): `gbrain sources current` + tier attribution (#1222)

Federated-brain users running destructive ops (extract, import,
purge) need a way to verify which source they're targeting BEFORE
the op runs. Pre-fix, the only way was to grep config files or run
the op with --dry-run and inspect output.

New command:
  gbrain sources current             # human output
  gbrain sources current --json      # machine-readable
  gbrain sources current --source X  # show what an explicit --source
                                     # X would resolve to (validates
                                     # X exists in the sources table)

Output names BOTH the resolved source id AND which tier of the 6-tier
resolution chain won (flag / env / dotfile / local_path /
brain_default / seed_default), plus a `detail` line naming the
winning signal (e.g. "GBRAIN_SOURCE=dept-x" or ".gbrain-source" or
"/work/gstack/src").

Implementation:
- New `resolveSourceWithTier()` in source-resolver.ts as an additive
  variant of `resolveSourceId()`. Walks the same 6 steps in the same
  order; just returns `{ source_id, tier, detail? }` instead of bare
  string. Existing `resolveSourceId()` unchanged — all callers
  continue working.
- New `SOURCE_TIER_NAMES` const + `SourceTier` type export so the
  CLI, doctor (Tier 5 follow-up), and future MCP consumers share one
  vocabulary instead of inlining strings.
- Help text updated; `current` subcommand registered in dispatcher.

11 new tests pin the 6-tier ladder + priority semantics. Existing
19 source-resolver tests still pass (regression preserved).

Per codex CF3 (the existing src/core/source-resolver.ts was missed
in the original plan). Re-uses the existing helper instead of
inventing a duplicate.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(extract): --source-id scopes extraction to one brain source (#1204)

Federated brain users running `gbrain extract` had no way to scope
extraction to one source. The DB path walks all sources together via
listAllPageRefs(), which is correct for cross-source resolution but
sometimes the user wants to extract per-source explicitly (e.g.
re-running extract on a specific source after a manual import).

The pre-existing `--source` flag is the data-source axis (fs|db) and
can't be repurposed. New flag `--source-id <id>` joins it on the
brain-source-id axis:

  gbrain extract all --source db --source-id alpha
    -> walks only alpha-source pages; extracts links + timeline
       from those, into the alpha source

Important: the resolver maps (allSlugs + slugToSources) stay built
from the FULL listAllPageRefs result, not the scoped subset. This
ensures qualified cross-source wikilinks like `[[other-src:slug]]`
still resolve correctly even when the extract walk is scoped — the
filter is on which pages we extract FROM, not what we can resolve TO.

Threaded through both `extractLinksFromDB` and `extractTimelineFromDB`
with backward-compat: callers passing no opts get the old behavior.

4 new test cases pin: walks-all-without-flag baseline,
alpha-only-when-scoped-to-alpha, beta-only-when-scoped-to-beta,
empty-set-on-unknown-source.

Note: #1204's wider "silent 0 links" report on federated brains has
additional facets beyond this flag (resolver path edge cases on
overlapping slugs). The scoped-walk fix gives users an explicit
workaround AND closes the per-source extraction gap.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* chore(todos): file v0.37.7.0 follow-ups (#1173, #1204, T5N)

Three items deferred from v0.37.7.0:

1. #1173 .sql indexing — verify-first gate found
   tree-sitter-sql.wasm missing from src/assets/wasm/grammars/.
   Dedicated wave needed: vendor the wasm, add .sql to walker
   filter, address slug-shape collision with #1172.

2. #1204 deeper investigation — wave added --source-id flag as
   workaround. Underlying silent-zero-links bug on unscoped
   federated extracts needs its own /investigate pass against
   a cross-source-duplicate-slug fixture.

3. Tier 5N doctor sweep for dead-lettered subagent jobs matching
   the #1151 fingerprint. Deferred to v0.37.8+ behind the islamabad
   doctor.ts conflict resolution.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(sync): walker skips git submodule directories (#1169)

Sync walker descended into git submodules and indexed their markdown
content as if it belonged to the parent brain. Users with submodules
in their brain repo saw foreign content in their pages table.

Fix: pruneDir gains an optional `parentDir` arg. When set, the helper
stats `<parentDir>/<name>/.git` and skips the directory if `.git`
exists as a FILE (gitfile pointer — the canonical submodule shape).
Directories containing `.git` as a DIRECTORY (a real nested repo,
not a submodule) are descended into; the inner `.git` dir itself is
then dot-prefix-excluded.

Callers updated to pass parentDir:
- src/commands/extract.ts walkMarkdownFiles
- src/core/cycle/transcript-discovery.ts walker

Back-compat preserved: existing pruneDir(name) callers without
parentDir get the pre-v0.37.7.0 behavior unchanged.

Companion `.gitignore`-respect feature from PR #1159 (@jetsetterfl)
NOT in this wave — it would require adding the `ignore` npm package
as a dep, which the plan's "no new deps in this PR" gate excludes.
Filed as follow-up TODO for a dedicated wave.

5 new test cases pin the submodule shape + back-compat + nested-repo
ambiguity. Existing extract-fs / extract-db tests unchanged.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(brain-routing): document 6-tier source resolution chain (#1222)

The convention skill didn't have a tier-by-tier reference for how
gbrain resolves the active source. Users running federated brains
had to read the source code to know which signal wins.

Added:
- Canonical 6-tier table (flag → env → dotfile → local_path →
  brain_default → seed_default) matching src/core/source-resolver.ts.
- Pointer to `gbrain sources current` (new in v0.37.7.0) as the
  verification command.
- The CLI-layer trust boundary note: operations.ts handlers don't
  read env/dotfile (preserves v0.34.1.0 source-isolation work for
  MCP callers).
- Per-command flag map: --source, --source-id (extract), and
  --include-foreign (graph-query).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(import): --source-id flag routes pages to a brain source (#1167)

`gbrain import --source dept-x ./pages` silently fell back to the
default source because the CLI parser never consumed --source. PR
#707's design intent excluded the flag explicitly; users had no
signal their pages were going to the wrong place. #1167 + #1222
filed the regression.

Fix: parse `--source-id <id>` (matching v0.37.7.0 extract.ts T2's
naming convention — --source-id stays out of conflict with future
axes that may want --source). When set, the flag value wins over
any programmatic opts.sourceId; back-compat preserved for callers
that pass sourceId via opts only.

Also threaded into the positional-dir arg parser's flagValues set
so `--source-id <value> <dir>` doesn't treat <value> as the dir.

Note on related surfaces:
- `gbrain query "X" --source_id dept-x` already routed correctly
  via the operations.ts query op (added in v0.34) — no fix needed.
- `gbrain extract --source-id <id>` shipped in T2.
- `gbrain sync --source <id>` already worked (pre-existing).
- `gbrain sources current` (shipped in T4) is the verification
  tool — run it before destructive ops to confirm routing.

Closes the silent-fallback for the import path. Co-authored with
@tyad67-netizen (#1168), @hnshah (#1124, #1120), whose patches
informed the shape; re-implemented against current master per
the wave's "re-implement, credit, close" workflow.

3 new test cases pin: default-without-flag, --source-id-routes-correctly,
flag-value-not-treated-as-dirArg.

Co-Authored-By: tyad67-netizen <noreply@github.com>
Co-Authored-By: hnshah <noreply@github.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(autopilot): reconnect classifier + launchd ThrottleInterval (#1162)

Pre-fix: when database_url was unset/malformed, the DB-health-check
reconnect loop logged `config.database_url undefined` forever
because the catch swallowed every error type uniformly. launchd's
KeepAlive=true respawned immediately on any exit, so even when
the process did exit, it came right back into the same bad state.
@colin477 reported the daemon-thrash pattern.

Two-part fix:

1. In-process error classifier — `classifyReconnectError(err)`:
   - `unrecoverable` (database_url missing/empty/malformed, auth
     failure, no-brain-configured): exit immediately with a clear
     stderr line. Pattern-matched against postgres / config-loader
     error shapes. Tests pin the matcher against the #1162
     fingerprint exactly.
   - `recoverable` (network blip, pool saturated, connection refused
     on a port coming up, Supabase 503): retry. Up to
     GBRAIN_AUTOPILOT_MAX_RECONNECT_FAILS (default 30 = ~5min) before
     finally giving up with `max_reconnect_fails_exceeded`.
   - Counter resets on every successful health probe or reconnect.

2. launchd plist gains `ThrottleInterval=60`. Combined with the
   in-process exit, launchd waits 60s before relaunching instead
   of immediate respawn. Pure-function `generateLaunchdPlist()`
   exported for tests.

16 new test cases:
- 11 classifier cases (database_url shapes, malformed URL, auth,
  role-does-not-exist with quoted name, network blip, pool
  saturated, 503, non-Error inputs, case-insensitivity)
- 5 plist generator cases (ThrottleInterval=60, KeepAlive
  preserved, wrapper path, XML escaping, StandardErrorPath).

Pre-existing autopilot-lock-path tests unchanged — both fixes
land cleanly side-by-side.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(oauth): confidential clients via custom /token middleware (#1166)

v0.34.1.0 (#909) fixed PUBLIC PKCE clients (client_secret=undefined)
by normalizing NULL → undefined in getClient. Confidential clients
regressed: the MCP SDK's clientAuth middleware does plaintext
`client.client_secret !== presented_secret` compare, but gbrain
stores SHA-256 hashes, so the SDK's compare always failed for
authorization_code and refresh_token grants on confidential clients.
Result: /token returned `invalid_client` for every confidential
exchange.

Fix shape per locked-decision-5: custom /token middleware BEFORE the
SDK's authRouter, similar to the pre-existing client_credentials
handler. The middleware:

1. Detects confidential auth via `client_secret` in body
   (client_secret_post) OR `Authorization: Basic` header
   (client_secret_basic per RFC 6749 §2.3.1).
2. Falls through to the SDK when neither is present (public PKCE
   path stays canonical, preserves v0.34.1.0 behavior).
3. Calls new `verifyConfidentialClientSecret(clientId, presented)`
   on the provider which does SHA-256 hash compare ourselves
   (same shape as exchangeClientCredentials' existing hash check).
4. On verification success, calls existing
   `exchangeAuthorizationCode` / `exchangeRefreshToken` directly
   with the validated client.
5. RFC 6749 §5.2 error semantics: 401 invalid_client for auth
   failures, 400 invalid_grant for code/token problems.

Per CLAUDE.md "GBRAIN:RLS_EXEMPT" annotation contract: this surface
sits in front of the SDK's clientAuth and doesn't depend on the
SDK's plaintext compare working — the SDK's middleware never
fires for confidential paths the new middleware claims.

7 new test cases pin: correct-secret-returns-client, wrong-secret
opaque rejection, non-existent client, public-client refuses
the confidential path, case-sensitivity, soft-deleted revocation,
verify-then-exchange-refresh round-trip with second-use rejection.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat(doctor): 3 new checks — source routing + oauth + autopilot lock (T12/T13/T14)

Three v0.37.7.0 doctor checks landing in one atomic commit (single
file, shared merge-conflict surface with garrytan/islamabad-v3 per
locked decision 1):

1. source_routing_health (T12 / #1167):
   Sample non-default sources for pages; warn when a registered
   source has zero pages (silent-collapse-to-default fingerprint).
   D5 lock: total-sample cap of 200 pages across all sources, with
   per-source cap = min(50, ceil(200/N)) so a 20-source CEO brain
   pays 200 selects, not 1000. Fix hint paste-ready to
   `gbrain sources current --json` for verification.

2. oauth_confidential_client_health (T13 / #1166):
   Probe every oauth_clients row. Confidential clients (auth_method
   != 'none') must have a non-NULL client_secret_hash; if any row
   claims confidential auth but stores NULL hash, that's the
   pre-v0.37.7.0 regression. Public clients (auth_method='none')
   correctly keep NULL hash per v0.34.1.0 #909. Fix hint:
   `gbrain auth revoke-client + register-client` OR `gbrain upgrade`.
   Pre-OAuth schemas (missing oauth_clients table) skip gracefully.

3. autopilot_lock_scope (T14 / #1226):
   Detect stale ~/.gbrain/autopilot.lock outside the current
   GBRAIN_HOME. Codex CF11: dangerous to paste-ready `rm` without
   verifying the owning PID isn't a live process. Hint reads the
   PID file and gives the user a `ps -p <pid>` check before any
   delete — matches sshd-style stale-lock recovery hints.

9 new test cases pin the canonical paths. Pre-existing 80+ doctor
checks unchanged.

Expected to conflict with garrytan/islamabad-v3 at merge time. The
3 new check functions live in their own block far from the
islamabad skill_brain_first check; the conflict surface should be
limited to the `checks.push(...)` call site near the end of
runDoctor's DB-checks phase (~10 lines).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(test): withEnv wrapper in source-resolver-with-tier (test-isolation lint)

The new source-resolver-with-tier.test.ts from T4 mutated
process.env.GBRAIN_SOURCE directly in two cases, which violates
scripts/check-test-isolation.sh R1 (env mutations leak across
parallel-loaded test files in the same shard process).

Fix: wrap both mutation sites in withEnv() from test/helpers/with-env.ts,
which saves+restores via try/finally per the canonical pattern in
CLAUDE.md.

Pure refactor — all 11 cases still green.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs: update project documentation for v0.37.7.0

CHANGELOG.md — populated the "What landed" stub with the 18-commit
brisbane wave (source-id flag threading, sources current subcommand,
graph-query foreign-edge footer, autopilot lockfile scope + reconnect
classifier + launchd ThrottleInterval, OAuth confidential client
middleware, reindex-frontmatter connect fix, subagent terminal-on-resume
fix, sync walker submodule skip, 3 new doctor checks, brain-routing.md
convention skill). Voice: ELI10 lead, capability table, paste-ready
verification, "what's safe to know" + "what we caught" sections.

CLAUDE.md — extended Key Files annotations for the v0.37.7.0 changes:
import/extract --source-id flags, sources current subcommand, graph-query
--include-foreign, resolveSourceWithTier() additive helper, autopilot
classifyReconnectError + generateLaunchdPlist exports, OAuth confidential
client middleware, pruneDir submodule detection, subagent terminal
short-circuit, 3 new doctor checks. Pinned by their test files.

llms-full.txt — regenerated via `bun run build:llms` (CI guard at
test/build-llms.test.ts will fail otherwise).

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

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-authored-by: rafaelreis-r <noreply@github.com>