…ems #6 + #7) (#1544)

* feat(doctor): doctor-categories foundation — BRAIN/SKILL/OPS/META sets + drift guard

Categorizes every doctor check name into exactly one of four categories. Exported
constants + categorizeCheck(name) helper are the single source of truth for the
v0.41.20.0 brain_checks_score + category_scores + --scope=brain wave. Drift guard
test parses doctor.ts source for both inline {name: 'foo'} and helper
const name = 'foo' patterns; CI fires if any check name lacks a category.

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

* feat(doctor): brain_checks_score + category_scores + --scope=brain skip-computation

Extends Check with optional category and DoctorReport with brain_checks_score +
category_scores (additive — schema_version stays at 2; back-compat health_score
math byte-identical). buildChecks gains --scope=brain with explicit early-skip
gates around the SKILL check group (resolver_health + skill_conformance +
skill_brain_first + whoknows_health). Sub-second doctor on a brain with thousands
of skills. computeDoctorReport tags every check via categorizeCheck() at compute
time. Human output leads with the brain figure and renders the weighted
BrainHealth.brain_score alongside.

Test seam fix in test/doctor-home-dir-in-worktree.test.ts: the pre-existing
fragile JSON parser walked back from "checks" to find the envelope's outer
brace; v0.41.20.0's new nested category_scores object broke that heuristic.
Anchored on the canonical {"schema_version" envelope prefix instead.

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

* feat(status): gbrain status — single-screen brain health dashboard + get_status_snapshot MCP op

NEW gbrain status command (src/commands/status.ts) composes 6 sections:
sync (per-source last_sync_at + staleness via buildSyncStatusReport),
cycle (TWO rows: last autopilot-cycle + last autopilot-* of any kind —
reflects v0.36.4.0 health-aware autopilot's targeted handler routing;
totals read from result.report.totals per the canonical handler shape),
locks (gbrain_cycle_locks active rows), workers (readSupervisorEvents +
summarizeCrashes), queue (LIVE counts NO time-window — old stuck jobs
are exactly what status surfaces), autopilot (PID liveness via kill -0).

Stable --json envelope (schema_version: 1). Exit codes 0=ok / 1=snapshot
failed / 2=usage. --section filter.

Thin-client mode routes Sync + Cycle through NEW get_status_snapshot MCP
op (admin scope, NOT localOnly; payload deliberately omits Locks /
Workers / Queue / Autopilot so feature creep can't quietly widen the
admin-scoped data exposure). Local-only sections render "local-only —
N/A on remote brain" honestly instead of pretending the local install's
empty state is the remote brain's.

CLI dispatch: pre-engine-bind branch for thin-client (no PGLite needed)
+ engine-connected dispatch case for local mode. CLI-only architecture
per codex MAJOR-4 (status owns its own thin-client branch inside
runStatus, not routed through op dispatch).

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

* chore: bump version to v0.41.20.0 + CHANGELOG + TODOS + llms regen

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

* fix(doctor-categories): categorize batch_retry_health from v0.41.19.0 Supavisor wave

The drift guard correctly caught a new check introduced by master's v0.41.19.0
Supavisor Retry Cathedral (PR #1537). batch_retry_health surfaces batch-write
retry events from the new src/core/audit/batch-retry-audit.ts module — OPS
category (infrastructure liveness).

This is exactly why the drift guard exists: any future check added to doctor.ts
without a category entry fails CI immediately instead of silently degrading
to 'meta'.

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

---------

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

Resolve VERSION, package.json, CHANGELOG conflicts. v0.41.22.0 stays
on top (higher than master's v0.41.20.0); master's v0.41.20.0 entry
preserved below in CHANGELOG order. Brought in master's gbrain status
+ doctor --scope=brain (PR #1544) and the v0.41.19.0 Supavisor Retry
Cathedral (PR #1537) cleanly via auto-merge.

Typecheck clean. bun run verify: 28/28 checks pass.

* upstream/master:
  v0.41.26.1 fix: lock-renewal cathedral — closes ~39 worker crashes/day (supersedes garrytan#1567) (garrytan#1572)
  v0.41.26.0 fix: dream --source + ingest junk titles + emoji-crash (supersedes garrytan#1559, garrytan#1561) (garrytan#1571)
  v0.41.25.0 perf(sync): batched deletes + global page-generation clock (supersedes garrytan#1538) (garrytan#1566)
  v0.41.24.0 fix(conversation-parser): threshold gates + bold-paren-time pattern — 20,167 Circleback messages unblocked (closes garrytan#1533) (garrytan#1543)
  v0.41.23.0 feat: extract operator surfaces + pack-driven extractables (garrytan#1541)
  v0.41.22.1 feat: brainstorm/lsd judge fixes (closes garrytan#1540 end-to-end) (garrytan#1562)
  v0.41.22.0 feat: type-unification cathedral — 94 types → 15 canonical (closes garrytan#1479) (garrytan#1542)
  v0.41.21.0 feat(ops): 5 daily-driver pains fixed in one wave (garrytan#1545)
  v0.41.20.0 feat: gbrain status + doctor --scope=brain (fix wave 2: items garrytan#6 + garrytan#7) (garrytan#1544)
  feat: v0.41.19.0 Supavisor Retry Cathedral (garrytan#1537)
  v0.41.18.0: gbrain onboard — the activation surface gbrain didn't have before (garrytan#1521)
  v0.41.17.0 feat: --workers N on every bulk command + facts dim doctor parity (garrytan#1519)
  v0.41.16.0 feat: conversation parser cathedral + progressive-batch primitive (closes garrytan#1461) (garrytan#1510)
  v0.41.15.0 feat(sync): --timeout + --max-age + partial status (closes garrytan#1472 RFC) (garrytan#1506)

… — gbrain extract --stale + doctor lag check (#1696) (#1755)

* feat(extract): link/timeline extraction freshness watermark (#1696)

Closes the "imported != curated" gap: plain `gbrain sync` only extracts
CHANGED pages, so a brain with autopilot off accumulated a links table that
was ~99.7% untyped `mentions` with nothing surfacing it. Adds a per-page
freshness watermark (pages.links_extracted_at, migration v112) and three
things built on it:

- `gbrain extract --stale [--source-id] [--catch-up] [--dry-run] [--json]`:
  incremental DB-source link+timeline sweep over pages whose extraction is
  stale (never extracted, edited since, or extractor version bumped). Small
  byte-bounded batches, non-swallowing flush, stamp-after-flush so a crash
  re-extracts idempotently. Stamps with the row's READ updated_at (not now())
  so a concurrent edit during the sweep stays stale instead of being lost.
- `links_extraction_lag` doctor check (local + remote): warn-only by default
  (>20%), hard-fail only via GBRAIN_EXTRACTION_LAG_FAIL_PCT. Vacuous-skip
  <100 pages; pre-v112 brains graceful-skip.
- `gbrain sync --no-extract` flag + end-of-sync nudge (fires on
  synced|first_sync|up_to_date so the initial import surfaces its backlog).

Three new BrainEngine methods (countStalePagesForExtraction /
listStalePagesForExtraction / markPagesExtractedBatch) with Postgres<->PGLite
parity + bootstrap probes. Schema parity: schema.sql + regenerated
pglite-schema.ts + schema-embedded.ts + bootstrap-coverage test. Migration
v112 (composite (source_id, links_extracted_at) index, no backfill so the
real backlog surfaces on first doctor run).

* test(audit): hermetic GBRAIN_AUDIT_DIR override for prune ENOENT case

The "no-op when audit dir does not exist (ENOENT)" case called
pruneOldBatchRetryAuditFiles without a GBRAIN_AUDIT_DIR override, so it read
the developer's real ~/.gbrain/audit and flaked (kept>0) on any machine with
prior gbrain audit history. Point it at a guaranteed-nonexistent temp path so
it tests the real missing-dir branch hermetically — matching the file
header's "never touches ~/.gbrain/audit" contract. Pre-existing flake
(introduced by v0.41.19.0 #1537), unrelated to #1696.

* chore: bump version and changelog (v0.42.2.0)

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

* docs: CLAUDE.md key-files entry for the #1696 extract-stale wave + regen llms-full

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