…finding #2)

Pre-fix: src/commands/doctor.ts contained two CLI-shaped functions
(runRemediationPlan + runRemediate) with hardcoded argv parsing,
process.exit calls, and console.log emission. Onboard CLI shell and the
upcoming MCP run_onboard op couldn't compose against them — the plan
file's "100-LOC thin wrapper" assumption didn't survive codex's review
of the actual source.

Post-fix: src/core/remediation/ exports a library shape that all three
consumers (doctor CLI, onboard CLI, MCP run_onboard) wrap.

  src/core/remediation/types.ts
    RemediationPlanOpts, RemediationPlan, RemediationOpts,
    RemediationResult, StepResult, RemediationHooks (the observability
    seam — library never calls console.* itself).

  src/core/remediation/context.ts
    loadRecommendationContext moved verbatim from doctor.ts. Re-exports
    RecommendationContext from brain-score-recommendations.ts since
    that's still the canonical home for the type (consumed by
    computeRecommendations).

  src/core/remediation/plan.ts
    computeRemediationPlan(engine, opts): Promise<RemediationPlan>.
    Pure read; produces the stable JSON envelope downstream agents
    bind to. Pulls in computeRecommendations + classifyChecks +
    maxReachableScore behind one library entry point.

  src/core/remediation/run.ts
    runRemediation(engine, opts, hooks): Promise<RemediationResult>.
    Orchestrator with BudgetTracker, checkpoint resume, D5 dep
    cascade, D7 per-step recheck. Returns a result object instead
    of process.exit calls; the CLI shell maps result.budget_exhausted
    / .target_unreachable / .submitted to exit codes.

  src/core/remediation/index.ts
    Barrel for the three modules above.

doctor.ts is now a thin wrapper:
  runRemediationPlan: parse argv → computeRemediationPlan → human/JSON render
  runRemediate: parse argv → TTY confirm gate → runRemediation(hooks: console.*)
The TTY confirmation step deliberately stays in the CLI shell — the library
never asks for confirmation; that's a CLI concern.

Net: ~340 LOC removed from doctor.ts; ~470 LOC added across the library
module (with full JSDoc + per-A-decision rationale comments). Functional
behavior preserved bit-for-bit: 67 tests pass across doctor.test.ts +
v0_37_gap_fill.serial.test.ts.

The Lane E.4 source-text test (test/v0_37_gap_fill.serial.test.ts:329)
followed loadRecommendationContext to its new home at
src/core/remediation/context.ts — assertions otherwise unchanged.

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

…tras (A2, codex finding #3)

Pre-fix: computeRecommendations at brain-score-recommendations.ts:170 was a
hardcoded planner for 5 synthetic check categories. Adding a Check.remediation
field to a new doctor check would NOT auto-wire into --remediation-plan —
the planner simply ignored it. Codex caught this when reviewing the plan's
"checks ARE specs" framing.

Post-fix: optional third arg `extraRemediations: RemediationStep[]` lets
callers inject step entries discovered outside the hardcoded planner. The
existing 5-category surface is preserved bit-for-bit; on id collision the
hardcoded entry wins, so an extra accidentally duplicating a hardcoded id
doesn't shadow legacy behavior.

RemediationPlanOpts gains the matching field; computeRemediationPlan in
src/core/remediation/plan.ts threads opts.extraRemediations through. The
4 new doctor checks (T4) will produce per-check helper functions that
return RemediationStep[]; onboard's render layer (T12) aggregates them
into the opts.extraRemediations slot. doctor's existing
--remediation-plan call passes empty (no behavior change for legacy CLI).

84 tests pass across brain-score-recommendations + doctor suites.

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

…imeline_coverage, takes_count) (A16, T4)

Adds src/core/onboard/checks.ts: 4 check helpers + a runAllOnboardChecks
aggregator. Each helper returns {check, remediations}, so doctor pushes
the Check entry (for human/JSON rendering) AND onboard's plan path
collects the RemediationStep[] (via T3's new extraRemediations seam in
computeRecommendations).

embed_staleness: COUNT(*) on content_chunks WHERE embedding IS NULL.
  Cheap thanks to content_chunks_stale_idx partial (v100).
  warn at 1+ stale, fail at 1000+; remediation points at embed-catch-up
  handler (built in T6).

entity_link_coverage: fraction of entity pages with inbound links.
  Per A21 + codex #15: TABLESAMPLE BERNOULLI on PG when total_pages > 50K
  with pinned sample formula (LEAST 100, GREATEST 2, target ~5000 rows)
  AND ±sqrt(p(1-p)/n) confidence interval embedded in message
  ("coverage: 31% ± 1.3%") so warn/fail decisions show their margin of error.
  PGLite path: full scan (rare >50K).
  warn <70%, fail <40%; remediation points at extract-ner handler.

timeline_coverage: same TABLESAMPLE policy. warn <90%, fail <70%;
  remediation points at extract-timeline-from-meetings handler.

takes_count: COUNT(*) on takes table. Per A12 two-gate consent: the
  remediation only emits when `takes.bootstrap_enabled` config is true.
  Otherwise the check shows "0 takes (takes.bootstrap_enabled is false;
  opt in to enable)" without an autopilot-eligible remediation. Prevents
  unattended LLM-bearing extractions on brains that haven't opted in.

runDoctor wires runAllOnboardChecks at the end of the DB-checks block
(after stale_locks); fast-mode skipped to preserve --fast UX.

Thin-client parity (A16 spec) deferred to T16 — the MCP run_onboard op
will run these helpers server-side where engine.executeRaw works,
which is the real federated path. Adding them to doctor-remote.ts
would duplicate the logic without functional benefit since the helpers
are server-side queries.

55 doctor tests pass; typecheck clean.

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

…nal (A13/A20, codex #7 #9)

Two interface extensions on BrainEngine, with parity across postgres-engine
and pglite-engine. Plus a follow-on fix for v99's timeline_entries dedup
widening.

listStaleChunks gains:
  - orderBy?: 'page_id' | 'updated_desc' (default 'page_id' = legacy)
  - afterUpdatedAt?: string | null (composite cursor for updated_desc)

When orderBy === 'updated_desc' the query JOINs pages and orders by
  p.updated_at DESC NULLS LAST, p.id ASC, cc.chunk_index ASC
backed by idx_pages_updated_at_desc + content_chunks_stale_idx partial
(both indexes added in v100). The cursor "next row" semantic with DESC
NULLS LAST + ASC tiebreakers is:
  (updated_at < prev) OR
  (updated_at = prev AND page_id > prev_page_id) OR
  (updated_at = prev AND page_id = prev_page_id AND chunk_index > prev_chunk_index)
First page (afterUpdatedAt undefined AND afterPageId 0) bypasses the
cursor predicate. Both engines parity-tested via 100/100 pglite-engine
tests; Postgres path mirrors the same WHERE clause structure.

executeRaw gains:
  - opts?: {signal?: AbortSignal}

Postgres impl: real cancellation via postgres.js's .cancel() on the
pending query. Pre-aborted signal short-circuits before the network
round-trip; mid-flight abort fires .cancel(). The query throws on
abort which the caller catches.

PGLite impl: in-process WASM has no kernel-level cancellation.
Best-effort: pre-check, then race the query against a signal-rejection
promise. The query keeps running in WASM but the awaited result is
discarded (DOMException AbortError thrown). Documented gap.

ReservedConnection.executeRaw extends the signature for type
compatibility but doesn't wire the signal (its only callers are
migrations + cycle-lock writes that explicitly don't want cancellation).

V99 timeline dedup follow-on: the dedup widening in migration v99
changed the unique index from (page_id, date, summary) to
(page_id, date, summary, source). The ON CONFLICT clauses in both
engines' addTimelineEntriesBatch + addTimelineEntry impls were still
using the old 3-tuple, causing 12 PGLite tests to fail with SQLSTATE
42P10 "no unique constraint matching ON CONFLICT specification".
Updated all 4 sites (2 per engine) to the 4-tuple.

Typecheck clean, 100/100 PGLite engine tests pass.

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

…tch-up handler (A13)

CLI surface on gbrain embed gains 3 flags:
  --batch-size N       Override hardcoded PAGE_SIZE=2000 (clamped 1..10000)
  --priority recent    Walk stale chunks newest-first (page.updated_at DESC)
                       backed by content_chunks_stale_idx + idx_pages_updated_at_desc
                       via T5's listStaleChunks(orderBy='updated_desc') extension.
                       Composite cursor (updated_at, page_id, chunk_index).
  --catch-up           Removes the GBRAIN_EMBED_TIME_BUDGET_MS wall-clock cap;
                       loops until countStaleChunks() returns 0.

EmbedOpts gains matching fields; embedAll + embedAllStale plumb them through.
The cursor tracking in embedAllStale now advances (afterUpdatedAt, afterPageId,
afterChunkIndex) instead of just (afterPageId, afterChunkIndex) when in
'updated_desc' mode. The engine returns p.updated_at as Date|string; the
caller normalizes to ISO string for the next page's cursor.

New Minion handler `embed-catch-up` registered in jobs.ts. Wraps runEmbedCore
with stale=true + catchUp=true + the priority/batchSize the caller supplies.
NOT in PROTECTED_JOB_NAMES (embedding spend only — same posture as the
existing embed-backfill handler). Consumed by the gbrain onboard remediation
pipeline (T11) when embed_staleness check fires.

63 embed tests pass; typecheck clean.

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

…10, T7, codex #12)

NEW src/core/extract-ner.ts: extractNerLinks(engine, opts). Walks pages,
reuses the by-mention gazetteer, applies the active schema-pack's
link_types[].inference.regex patterns to assign a typed verb to each
mention ("CEO of Acme" + Acme is a company → 'works_at' linking the
source page to Acme).

Codex finding #12 design: do NOT split link_source='ner' as a new
provenance. NER is still mention-derived; splitting would break every
existing link_source='mentions' query (backlink-count, orphan-ratio,
doctor checks). Instead: keep link_source='mentions' AND set
link_kind='typed_ner' (v98 column).

LinkBatchInput type gains link_kind field. Both engines'
addLinksBatch impls add the column to the INSERT projection + unnest()
tuple (column #11). The links UNIQUE constraint excludes link_kind so
an existing plain mention row + a typed_ner row for the same (from, to,
type, source, origin) collide DO NOTHING; the typed link goes in as a
separate row with a DIFFERENT link_type (the inferred verb), so they
don't collide on the typical case.

CLI: `gbrain extract links --ner` (DB source only). Combined
`--by-mention --ner` walk shares ONE gazetteer build across both passes
— saves a full walk on big brains. Either flag alone runs its pass
solo. Each gets its own --source-id filter inheritance.

Minion handler: `extract-ner` (NOT in PROTECTED_JOB_NAMES — regex-only,
no LLM spend). Consumed by onboard's entity_link_coverage remediation
when coverage <70%.

Target-type lookup: one round-trip SELECT slug, source_id, type FROM
pages WHERE type IN ('person', 'company', 'organization', 'entity')
AND deleted_at IS NULL — built once at extraction start, consulted
per-mention. Avoids the N+1 getPage cost.

Pack best-effort: when no active pack OR no link_types declared OR
no inference.regex on any link_type, returns pack_unavailable=true and
0 created. CLI prints a one-line note; handler returns silently.

122 tests pass (pglite-engine + by-mention); typecheck clean.

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

…m-meetings (A11, T8, codex #11)

NEW src/core/extract-timeline-from-meetings.ts:
extractTimelineFromMeetings(engine, opts). Walks meeting pages, finds
discussed entities via two sources, writes a timeline entry on each
entity page.

Discussed-entity sources merged:
  1. Existing 'attended' links from the meeting (canonical attendees).
     One round-trip SELECT pulls all attended edges for the loaded
     meeting set; in-memory Map<meetingSlug → attendees[]> for O(1)
     lookup per meeting.
  2. Body-text mentions via the existing by-mention gazetteer
     (findMentionedEntities + cross-source guard). Catches entities
     discussed in the meeting body even when no explicit 'attended'
     link exists.

De-duped via Map<sourceId::slug → entity> within each meeting so a
person who's both an attendee AND mentioned in the body gets exactly
one timeline row per meeting, not two.

Timeline write uses TimelineBatchInput with:
  source = 'extract-timeline-from-meetings:<meeting-slug>'
  summary = 'Discussed in <meeting-title>'
  date = meeting.effective_date

Per v99 dedup widening (codex #11): the source field is now in the
uniqueness key (page_id, date, summary, source). Two meetings on the
same date with the same summary on the same entity page survive as
distinct rows — the second meeting's provenance is no longer silently
dropped.

CLI: `gbrain extract timeline --from-meetings` (DB source only). Mode
dispatch — runs SOLO (does not combine with --by-mention/--ner; those
are links passes).

Minion handler: `extract-timeline-from-meetings` (NOT in
PROTECTED_JOB_NAMES — pure SQL + string scan). Consumed by onboard's
timeline_coverage remediation when coverage <90%.

Typecheck clean.

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

NEW src/core/extract-takes-from-pages.ts: Haiku classifier loop. Walks
pages WHERE type IN ('concept','atom','lore','briefing','writing',
'originals') AND deleted_at IS NULL AND length(compiled_truth) > 200,
ordered by updated_at DESC. Each page is truncated to 20K chars and
sent to Haiku with a strict-JSON classifier prompt:
  {"claim", "kind": fact|take|bet|hunch, "weight": 0..1}

Inserts via addTakesBatch with source='cli:takes-bootstrap-from-pages'.

Two-gate consent per A12:
  1. `takes.bootstrap_enabled` config (default false) — even the manual
     CLI refuses without it explicitly set.
  2. --yes flag (CLI) — interactive confirmation that this sends content
     to Haiku.

The handler-side gate also reads takes.bootstrap_enabled, so even a
trusted local Minion submitter (allowProtectedSubmit=true) cannot
fire takes-bootstrap on a brain that hasn't opted in.

CLI: `gbrain takes extract --from-pages [--yes] [--dry-run] [--source-id X]
[--max-pages N] [--holder name]`. Surfaces consent-gate-blocked vs
llm-unavailable distinctly so users see the actual blocker.

Minion handler `extract-takes-from-pages` added to PROTECTED_JOB_NAMES.
Consumed by onboard's takes_count remediation when count=0 AND
takes.bootstrap_enabled=true (handler-side double-check).

Per A24: ships with classifier infrastructure ONLY. Per-prompt eval suite
deferred to v0.42.1 follow-up; autopilot remediation tier for takes-bootstrap
stays manual_only until eval coverage catches up. Manual `gbrain takes
extract --from-pages --yes` is the only path that triggers it in v0.42.0.

parseClaimsJson exported for unit testing — strict JSON parse + ```json
fence strip + kind allowlist filter, returns [] on any parse failure.

Typecheck clean.

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

…bution (A7+A23, codex finding #4)

NEW src/core/minion-spend.ts: small primitive that closes the per-OAuth-
client spend chain gap codex flagged when MCP run_onboard submits child
Minion jobs.

Pre-fix: only subagent loops via budget-meter.ts recorded spend against
the originating OAuth client. Generic Minion handlers (embed-catch-up,
extract-ner, extract-timeline-from-meetings, extract-takes-from-pages)
wrote to the gateway with no per-client attribution — admin-scope tokens
would have unbounded indirect spend via the run_onboard fan-out.

Convention for v0.42.0 (deferred schema column to v0.42.1):
  - run_onboard MCP op sets job.data.client_id when submitting each
    child handler.
  - Handlers that spend LLM/embedding budget call
    recordMinionJobSpend(engine, job, {operation, spendCents, ...})
    which reads job.data.client_id and writes mcp_spend_log with
    the right attribution.
  - Local-submitted jobs (CLI, autopilot tick) pass no client_id;
    the row still lands with client_id=null for global accounting.

Two exports:
  getJobClientId(job): undefined for local jobs; the OAuth client_id
    string for MCP-submitted ones.
  recordMinionJobSpend(engine, job, entry): wraps recordSpend with
    job-aware attribution. Best-effort throughout — spend telemetry
    failures MUST NOT fail the user's call.

A23 full schema column (minion_jobs.client_id + index) deferred to
v0.42.1; today's JSONB-pass-through is sufficient for the MCP
run_onboard chain to land per-client attribution end-to-end. Handlers
adopt the primitive over time; no behavior change for callers that
haven't migrated.

Typecheck clean.

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

…6 + A25 + A17, T11)

NEW src/core/onboard/impact-capture.ts. Three exports:

captureMetric(engine, metric)
  Pure-ish: returns the current numeric value for one of 5 metrics
  (orphan_count, stale_count, entity_link_coverage, timeline_coverage,
  takes_count). Returns null on any throw per A17 best-effort posture
  — a stat-query failure MUST NOT block the extraction itself.

writeImpactLogRow(engine, attribution, metric, before, after, details?)
  Best-effort INSERT into v100's migration_impact_log table. Attribution
  columns (job_id, source_id, brain_id, started_at, idempotency_key,
  applied_by) per A25 + codex finding #10 so concurrent runs can't
  misattribute deltas.

withImpactCapture(engine, attribution, metric, runner, details?)
  Convenience: capture-before → run → capture-after → write log row.
  Per A17 the log row lands even when the runner throws (after-on-fail
  + error in details), so downstream consumers see a "ran but impact
  unknown" entry instead of silent loss.

Designed to be picked up by the 4 new Minion handlers (embed-catch-up,
extract-ner, extract-timeline-from-meetings, extract-takes-from-pages)
when they wrap their main runner. Handlers stay decoupled from the
log-write path — they just call withImpactCapture with the metric they
move. Per-handler integration follows in T12/T13/T15 as those wrappers
land.

Typecheck clean.

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

NEW src/core/onboard/types.ts: OnboardRecommendation (extends
RemediationStep with apply_policy + prompt_text + migration_id),
OnboardReport (stable JSON envelope), OnboardOpts.

NEW src/core/onboard/render.ts:
  toOnboardRecommendation(step): RemediationStep → OnboardRecommendation
    Sets apply_policy per A8 tiered rules:
      - protected + job === extract-takes-from-pages → 'manual_only' (A12/A24)
      - protected + other → 'prompt_required'
      - non-protected → 'auto_apply'
  buildOnboardReport(plan, opts?): assembles the stable JSON envelope.
  renderHuman(report): string. Echoes the "Recommendation + WHY" framing
    the CEO + Eng + Codex reviews settled on; CLI shell prints to stdout.

Stable JSON envelope shape:
  schema_version: 1
  brain_id?: string
  recommendations: OnboardRecommendation[]
  summary: { total, auto_eligible, prompt_required, manual_only,
             est_total_usd }
  history?: Array<{ remediation_id, metric_name, metric_before,
                    metric_after, delta, applied_at }>

Library-shaped — no console.* / process.exit. T13 (onboard CLI shell)
calls these from the wrapping CLI. MCP run_onboard (T16) returns the
JSON envelope unmodified.

Typecheck clean.

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

NEW src/commands/onboard.ts (~180 LOC). Thin wrapper that composes:
  - T2 library (computeRemediationPlan + runRemediation)
  - T4 onboard checks (runAllOnboardChecks → extraRemediations)
  - T12 render layer (buildOnboardReport + renderHuman)

Three modes:
  --check    (default): print plan, no submission. Computes plan via
             T2 library with T4 check-derived extraRemediations.
             Renders human (default) or JSON envelope (--json).
  --auto:    submit auto_apply tier. Requires --max-usd N (cron-safety
             per A12 + A20 — refuses without explicit cap to avoid
             surprise spend).
  --auto --yes: also submit prompt_required tier.
  --history: dump last 50 migration_impact_log entries.

Library hooks wired into stderr (per CLI/library separation): onStepStart,
onStepEnd, onBudgetRefused, onBudgetExhausted, onNothingToDo,
onTargetUnreachable. Final JSON envelope (--json) or human summary
lands on stdout.

CLI dispatch: registered in src/cli.ts CLI_ONLY set + case dispatch
between 'takes' and 'founder'.

Typecheck clean. Manual smoke-test pending T20 E2E (DATABASE_URL gated).

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

NEW src/core/onboard/init-nudge.ts exports two fail-open hooks:

runInitNudge(engine):
  Post-initSchema 5-query AbortSignal-bound parallel check against a
  3-second wallclock budget. Per A20: uses REAL cancellation via the
  T5 executeRaw signal extension — Promise.race against a timer was
  codex's #7 wrong shape. Postgres queries actually .cancel(); PGLite
  documented gap.
  Partial-results path: if some checks complete and the budget fires
  on others, prints what landed + a fallthrough hint pointing at
  `gbrain onboard --check` for the full picture.
  Per A18: fail-open — ANY throw is caught, logged to stderr, and
  suppressed so init returns successfully.
  Bypass: GBRAIN_NO_ONBOARD_NUDGE=1 short-circuits. Non-TTY default
  short-circuits too (CI/scripted callers see nothing).
  Nudge format: one-line summary of opportunities ("Brain has
  opportunities: 23000 stale chunks, link coverage 32%, 0 takes")
  + a 'gbrain onboard --check' nudge.

runUpgradeBanner(_engine):
  Lighter post-upgrade banner. Doesn't engine-query — just prints a
  one-line nudge that upgrades may surface new opportunities. Same
  fail-open posture.

Wired into:
  src/commands/init.ts:initPGLite (end-of-function, after reportModStatus)
  src/commands/init.ts:initPostgres (same)
  src/commands/upgrade.ts:runPostUpgrade (end-of-function, after
  postUpgradeReferenceSweep)

Each wire site uses dynamic import + try/catch so even an import
failure can't crash init/upgrade.

Typecheck clean.

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

… T15)

Pre-fix: autopilot tick's per-source recommendation walk called
computeRecommendations(health, ctx) — doctor's hardcoded 5-category
planner. The 4 new onboard checks (embed_staleness,
entity_link_coverage, timeline_coverage, takes_count) had nowhere to
hook in, so even with takes.bootstrap_enabled flipped on, autopilot
never noticed 0 takes and never proposed bootstrap.

Post-fix: tick body now ALSO calls runAllOnboardChecks(engine) and
threads the result's RemediationStep[] into the T3-generalized third
arg of computeRecommendations. The planner merges onboard's extras
with the legacy hardcoded entries (hardcoded wins on id collision).

Per A19 fail-open: any throw in the onboard-checks path is caught,
logged to stderr, and suppressed. The legacy plan (without extras)
runs as before — autopilot can't crash from an onboard-check failure.

A22 (idempotency-key dedupe across concurrent manual + autopilot
runs): inherits from the existing computeRecommendations →
remediation.idempotency_key chain. T7-T9 handlers each get their
content-hash key from the makeRemediationStep factory; an autopilot
tick + a manual `gbrain onboard --auto` submitting the same step
in the same brain produce the SAME key, so queue.add(...) dedupes.

No behavior change for brains where all 4 onboard metrics already
look healthy (extras=[]; legacy plan unchanged).

Typecheck clean.

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

…7, T16, codex finding #5)

NEW MCP op `run_onboard`. Admin scope (NOT localOnly) so federated /
thin-client brain installs can probe brain health + submit auto-eligible
remediation handlers over OAuth-authenticated MCP.

Two-tier authorization per A7 + codex #5:
  - Admin scope: sufficient for mode='check' (read-only OnboardReport JSON)
    AND for submitting non-protected handlers in mode='auto'/'auto-with-prompt'.
  - run_protected_onboard scope (NEW, additive): MUST be granted in
    addition to admin for any PROTECTED_JOB_NAMES handler to fire
    (synthesize, patterns, consolidate, extract-takes-from-pages,
    contextual_reindex_per_chunk).

Without the new scope tier, an admin-scoped OAuth token would silently
bypass the same protected-name gate `submit_job` enforces at
operations.ts:2288. The codex finding #5 caught this: admin scope alone
was insufficient guard. Now the run_onboard op explicitly FILTERS
protected extras from the recommendation plan when the caller lacks
run_protected_onboard; filtered items appear in the response as
skipped_missing_scope[] so the caller knows what would have been
available with the right grants.

Modes:
  check               — read-only OnboardReport JSON envelope.
  auto                — submits auto_apply tier (plus prompt_required
                        when --yes/auto-with-prompt).
  auto-with-prompt    — adds prompt_required tier.

Both auto modes REQUIRE max_usd per A12 + A20 cron-safety (rejects
with invalid_params if missing).

Per A26 source-scope: future extension will scope plans by ctx.sourceId
/ ctx.auth.allowedSources. Today the recommendation planner is
brain-wide; the source-scope thread doesn't change correctness, just
optimization.

Per A19 fail-open: any error in runAllOnboardChecks during plan-build
caught + suppressed; the plan still returns with extras=[] rather than
crashing the op.

Typecheck clean.

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

NEW scripts/check-source-scope-onboard.sh. Grep guard for SQL sites in
onboard surfaces (src/core/onboard/, src/commands/onboard.ts) that
touch source_id-bearing tables (pages, content_chunks, takes, links,
timeline_entries) WITHOUT either:
  (a) source_id / sourceIds in the WHERE clause, OR
  (b) the opt-out marker `sourcescope:brain-wide` within 4 lines above
      the SQL.

File-level opt-out: `sourcescope:file-brain-wide` in the file header
(first 30 lines) treats every SQL site in that file as intentionally
brain-wide. Used by onboard/checks.ts, onboard/impact-capture.ts, and
commands/onboard.ts because the onboard CHECKS are explicitly brain-wide
aggregates (orphan_count, stale_count, link_coverage are reported
across all sources by design).

Wired into bun run verify (23 checks total now, all green).

Without this gate, any future onboard SQL touching per-source data
without source-scoping would silently leak rows across sources —
exactly the class of bug v0.34.1's P0 seal closed at the engine layer.
The lint adds an explicit forcing function for new code in the onboard
surface.

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

Adds a v0.42.0+ section to INSTALL_FOR_AGENTS.md describing:
  - First-connect probe: gbrain onboard --check --json
  - Post-upgrade re-probe (after gbrain upgrade)
  - Unattended remediation: gbrain onboard --auto --max-usd 5
  - MCP run_onboard op for federated/thin-client installs
  - run_protected_onboard scope requirement for LLM-bearing handlers
  - Two-gate consent for takes-bootstrap (takes.bootstrap_enabled + --yes)
  - GBRAIN_NO_ONBOARD_NUDGE=1 bypass for CI

Per D13: agents should run --check on first connect AND after every
upgrade as a hygiene step. The autopilot path makes this auto-improve
on a 24h cycle; the explicit agent probe surfaces opportunities
immediately on connect rather than waiting for the next autopilot tick.

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

NEW test/e2e/onboard-full-flow.test.ts. 13 hermetic PGLite cases
(no DATABASE_URL needed) covering the key onboard contracts:

  captureMetric — all 5 metrics return expected values on empty brain
    (0 for counts; 1 for coverage = vacuous truth).

  runAllOnboardChecks — returns exactly 4 results with correct names;
    empty brain shows stale/link/timeline ok BUT takes_count warns
    (0 takes); 0 remediations emitted because takes.bootstrap_enabled
    defaults to false per A12 two-gate consent.

  computeRemediationPlan — extras (T3 generalization) thread through to
    plan.plan output; stable schema_version: 2 envelope.

  buildOnboardReport — stable schema_version: 1 envelope with the right
    summary fields populated.

  toOnboardRecommendation tier policy (A8):
    - non-protected job → auto_apply
    - extract-takes-from-pages → manual_only (A12 + A24)
    - other protected jobs (synthesize, patterns, ...) → prompt_required

Full DATABASE_URL-gated end-to-end (real Postgres, actual extractions
through Minion handlers) deferred to v0.42.1 once the per-handler test
seam lands; the hermetic suite covers the data-shape contracts that
matter for downstream consumers binding to the JSON envelopes.

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

…completes #1409)

VERSION + package.json bumped to 0.42.0.0. CHANGELOG with full ELI10 lead
+ "What you can do that you couldn't before" itemized list + "To take
advantage of v0.42.0.0" upgrade steps per CLAUDE.md voice rules.

TODOS.md: 9 follow-up items filed (TODO-A through TODO-I) for the
v0.42.1+ wave: pack-aware linkable types, LLM-disambiguation NER,
onboard --explain, live-brain impact measurement, 100+-case takes
classifier eval, admin SPA UI, full DATABASE_URL E2E, minion_jobs
client_id schema column, thin-client doctor-remote parity.

llms-full.txt regenerated per CLAUDE.md rule (every CHANGELOG edit
followed by bun run build:llms in the same commit).

23/23 verify checks pass.

Full implementation across 21 commits on this branch (T0-T21):
  T0  merge master
  T1  schema migrations v98/v99/v100
  T2  extract doctor remediation library
  T3  generalize computeRecommendations
  T4  4 new doctor checks
  T5  engine API: listStaleChunks orderBy + executeRaw AbortSignal
  T6  embed --batch-size / --priority recent / --catch-up
  T7  NER extraction + extract-ner handler
  T8  timeline-from-meetings + extract-timeline-from-meetings handler
  T9  takes-bootstrap + extract-takes-from-pages handler
  T10 recordMinionJobSpend primitive
  T11 impact capture module + writeImpactLogRow
  T12 onboard render layer (types + render)
  T13 gbrain onboard CLI shell
  T14 init nudge + upgrade banner
  T15 autopilot tick consults onboard
  T16 MCP run_onboard + run_protected_onboard scope
  T17 check-source-scope-onboard lint
  T18 INSTALL_FOR_AGENTS.md agent prescription
  T20 hermetic PGLite E2E (13 cases)
  T21 ship (this commit)

Reviews: CEO + Eng + Codex on plan
~/.claude/plans/system-instruction-you-are-working-lively-hollerith.md.
27 A-decisions locked; 18 codex findings absorbed.

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

Two CI fixes from PR #1521 + version renumber per user request.

Why fix #1 (connection-resilience.test.ts): T5/A20 extended
PostgresEngine.executeRaw signature to accept an optional
`opts?: { signal?: AbortSignal }` 3rd arg and rewrote the body as
multi-line. The regression test's regex was anchored to the legacy
single-line `(sql: string, params?: unknown[])` shape and the
assertions banned `try {` / `catch` (which T5 legitimately added for
AbortSignal cancellation swallow, NOT for retry). Updated regex to
tolerate both shapes; replaced the wrong `not.toContain('conn.unsafe(
sql, params')` assertion (which incorrectly flagged the legitimate
single call) with a count assertion: `conn.unsafe(` must appear
exactly ONCE in the body. Preserves the original D3 intent (no
per-call retry — recovery is supervisor-driven via reconnect()) while
accepting the new try/catch shape that swallows AbortSignal aborts.

Why fix #2 (src/core/onboard/checks.ts): Three of the four new
onboard doctor checks (entity_link_coverage, timeline_coverage,
embed_staleness) emitted `status = 'fail'` on healthy DBs that simply
hadn't run extractions yet. This flipped `gbrain doctor`'s exit code
to non-zero on freshly initialized brains, breaking
test/e2e/mechanical.test.ts:1280 ("gbrain doctor exits 0 on healthy
DB"). Downgraded all three to `status = 'warn'` — these are
remediation opportunities, not assertion failures. Doctor exit
codes are reserved for actual failures; remediation surfaces use
warn-level signaling so they can be picked up by `--remediate`
without polluting the exit code.

Why fix #3 (version renumber 0.42.0.0 → 0.41.18.0): Per user
directive, this wave ships as v0.41.18.0 rather than v0.42.0.0.
Master is at 0.41.16.0; 0.41.17.0 is reserved for an in-flight
wave. Renamed every reference my branch added (54 files touched):
VERSION, package.json, CHANGELOG.md header, TODOS.md, plus inline
version-stamp comments across src/, test/, and scripts/. Preserved
13 files with PRE-EXISTING `v0.42.0.0` references on master (from
earlier waves originally planned for v0.42 that landed at v0.41.x —
those stay as historical record). Verified via per-file diff against
origin/master: every renamed reference is one I added in this branch.

Audit trio aligned: VERSION=0.41.18.0, package.json=0.41.18.0,
CHANGELOG topmost entry=[0.41.18.0]. llms-full.txt regenerated to
match CLAUDE.md updates.

Bisect contract: this commit fixes CI test failures from PR #1521's
landing. Typecheck clean; connection-resilience suite 26/26 pass.

Refs A20 (executeRaw AbortSignal), A16 (4 new onboard checks),
codex #1 (master collision avoidance via renumber).

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

# Conflicts:
#	CHANGELOG.md
#	TODOS.md
#	VERSION
#	package.json
#	src/commands/extract.ts