fix(onboard): stop dropping onboard-check remediations on the --apply --auto path

Takeover of #2161. runRemediation ignored onboard-check extras in three
places: the pre-flight plan, the initial recommendation build, and the D7
mid-run recheck that rebuilds recs after every completed step. The --check
path threaded extras correctly, so `gbrain onboard --apply --auto` reported
"Nothing to do" when the only remediable work came from onboard checks —
and even with the first two sites fixed (the original PR diff), any plan
with 2+ steps dropped all remaining extras after step 1 via the recheck.

- Add RemediationOpts.extraRemediations; thread it through the pre-flight
  plan, initial recs, and the mid-run recheck.
- Recheck filters extras to ids not already processed this run: extras
  carry static status:'remediable', so unfiltered threading would resubmit
  completed extras forever.
- Wire the CLI --auto path (onboard.ts) AND the MCP run_onboard auto path
  (operations.ts), which already computed the scope-filtered allowedExtras
  and then dropped it.
- Regression test: extras-only plan on an empty brain runs BOTH extras
  exactly once and terminates (serial file: mock.module queue stub +
  GBRAIN_HOME tmpdir).

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

skills/article-enrichment/SKILL.md

@@ -85,10 +85,6 @@ gbrain get media/articles/<slug>
 
 # 5. Cross-link entities
 #    For every person/company mentioned, add a timeline back-link.
-#    Mark NEW pages minted for article subjects the reader only reads ABOUT
-#    (not personal contacts) as reference: `gbrain reference <slug>`
-#    (or reference: true in frontmatter). Exempts them from coverage nudges;
-#    they stay searchable. Default for real contacts: do NOT set it.
 ```
 
 ## Quality bar

skills/book-mirror/SKILL.md

@@ -273,13 +273,6 @@ Cross-link entities mentioned in the analysis:
 - For every person the right column references with a brain page, add a
   back-link from `people/<slug>` to the new `media/books/<slug>-personalized`
   page (per `conventions/quality.md` Iron Law).
-- **Mark book figures as reference entities.** Any NEW person/company page you
-  mint for a figure from the book (an author, a historical figure, a company
-  the book discusses) — someone the reader reads ABOUT but doesn't personally
-  interact with — should be flagged: `gbrain reference <slug>` (or
-  `reference: true` in frontmatter). They stay fully searchable/linkable but
-  are exempt from coverage nudges (timeline/links). Skip this for anyone the
-  reader actually knows. Default for normal contacts: do NOT set it.
 
 ## Quality bar (the bar)
 

skills/conventions/reference-entities.md

@@ -1,62 +0,0 @@
-# Convention: Reference entities (canon figures)
-
-Some person/company pages are people/orgs the user **reads about** but does not
-personally interact with — a book's author, a historical figure, a company an
-article discusses (Andy Grove, Kleiner Perkins, Intel…). They are real
-knowledge, worth a page, but they have **no dated history in the user's own
-life**, so the entity coverage metrics (`timeline_coverage`,
-`entity_link_coverage`) flag them as permanently incomplete with no honest fix.
-
-The `reference: true` frontmatter flag resolves this.
-
-## What it does
-
-- A page with `reference: true` is **exempt from the entity coverage metrics
-  only** (`timeline_coverage`, `entity_link_coverage`, and their onboard
-  nudges).
-- It keeps its real `type` (`person` / `company`), so it stays **fully
-  searchable, enrichable, linkable, and edge-resolvable**. NOTHING about
-  retrieval changes — this is the whole reason it's a flag, not a new `type`.
-- It is **opt-in**. Absent / `false` / anything-but-`true` = a normal entity
-  that DOES count toward coverage. **This is the default — do not set it on real
-  contacts.**
-
-## When to set it
-
-Set `reference: true` when the entity is a figure/org the user reads ABOUT, not
-someone they deal with:
-
-- authors and figures discussed in a book (book-mirror) or article
-  (article-enrichment)
-- historical / canon figures imported as reference knowledge
-- companies named only as examples in source material
-
-Do NOT set it for people the user actually meets, emails, or works with — those
-are normal entities whose missing timeline/links is a real, actionable gap.
-
-## How to set it
-
-```bash
-gbrain reference <slug>            # mark as reference
-gbrain reference <slug> --unset    # back to a normal entity
-```
-
-The command writes the flag to BOTH the markdown frontmatter (durable; survives
-re-ingest / engine rebuild — markdown is the source of truth) AND the engine
-JSONB (so coverage reflects it immediately, no re-sync). It's idempotent. You
-can also hand-edit frontmatter (`reference: true`) and re-ingest.
-
-## Why a flag, not a type
-
-A new `type: reference-person` would drop the page out of every
-`type IN ('person','company')` filter — search, enrichment, whoknows, link
-inference — so you'd lose the figure everywhere, not just the metric. The flag
-narrows the change to exactly the coverage denominators and nothing else.
-
-## Implementation
-
-`src/core/reference-flag.ts` — `referenceExclusionSql(alias?)` is the single
-source of truth for the predicate `(frontmatter->>'reference') IS DISTINCT FROM
-'true'`, ANDed into both numerator and denominator at every coverage site
-(getHealth in both engines, onboard/checks.ts, init-nudge.ts). Backed by the GIN
-index on `pages.frontmatter`.

skills/enrich/SKILL.md

@@ -268,18 +268,6 @@ Active items, pending decisions, things to track.
 - **YYYY-MM-DD** | Event description [Source: ...]
 ```
 
-### Reference entities (canon figures)
-
-If the entity is someone/something the user reads ABOUT but does not personally
-interact with — a book author, a historical figure, a company discussed in an
-article — mark the page as reference: `gbrain reference <slug>` (or
-`reference: true` in frontmatter). Reference pages keep their `person`/`company`
-type and stay fully searchable, enrichable, and linkable; they are only exempt
-from the entity coverage nudges (timeline/links) that don't apply to figures
-with no dated history in the user's own life. **Default: do NOT set it** — real
-people and companies the user deals with are normal entities. Full convention:
-`conventions/reference-entities.md`.
-
 ### Step 7: Cross-reference
 
 - Update company pages from person enrichment (and vice versa)

skills/maintain/SKILL.md

@@ -270,11 +270,6 @@ Populate them periodically or after major imports:
 - `gbrain stats` — verify `link_count > 0` and `timeline_entry_count > 0` after extraction.
 - `gbrain health` — review `link_coverage` and `timeline_coverage` percentages
   on entity pages (person/company). Below 50% means more extraction is needed.
-  Note: pages flagged `reference: true` (canon/reference figures the user only
-  reads about) are EXEMPT from these two metrics — if coverage looks stuck
-  because of book/article-imported figures with no real history, mark them with
-  `gbrain reference <slug>` rather than chasing the percentage. See
-  `conventions/reference-entities.md`.
 
 Available link types (use with `gbrain graph-query --type`):
 `attended`, `works_at`, `invested_in`, `founded`, `advises`, `mentions`, `source`.

src/cli.ts

@@ -54,7 +54,7 @@ export function bigintToStringReplacer(_key: string, value: unknown): unknown {
 }
 
 // CLI-only commands that bypass the operation layer
-export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'reference', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
+export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
 // CLI-only commands whose handlers print their own --help text. These are
 // excluded from the generic short-circuit so detailed per-command and
 // per-subcommand usage stays reachable.
@@ -1652,11 +1652,6 @@ async function handleCliOnly(command: string, args: string[]) {
         await runFiles(engine, args);
         break;
       }
-      case 'reference': {
-        const { runReference } = await import('./commands/reference.ts');
-        await runReference(engine, args);
-        break;
-      }
       case 'embed': {
         const { runEmbed } = await import('./commands/embed.ts');
         await runEmbed(engine, args);

src/commands/onboard.ts

@@ -142,12 +142,16 @@ export async function runOnboard(engine: BrainEngine, args: string[]): Promise<v
 
   // --auto path: runs through the T2 library orchestrator. Hooks emit CLI
   // progress to stderr; the final result lands as JSON on stdout (or human
-  // summary).
+  // summary). extraRemediations (gathered above from runAllOnboardChecks)
+  // is threaded into the runner so the onboard-check remediations
+  // (extract-ner, extract-timeline-from-meetings, etc.) reach the planner
+  // — the same wiring the --check path uses above.
   const result = await runRemediation(
     engine,
     {
       targetScore,
       maxUsd,
+      extraRemediations,
       // --auto --yes opts into the prompt_required tier too; library
       // doesn't distinguish auto_apply vs prompt_required, it just runs
       // every remediation in the plan. The plan-building side (T12 render)

src/commands/reference.ts

@@ -1,130 +0,0 @@
-// gbrain reference <slug> [--unset] [--brain <dir>] [--json]
-//
-// Mark (or unmark) a page as a reference-only entity. A reference page keeps its
-// real type (person/company) — fully searchable/enrichable/linkable — but is
-// exempt from the entity coverage metrics (timeline_coverage,
-// entity_link_coverage). See src/core/reference-flag.ts for the rationale.
-//
-// Durability: the flag is written to BOTH the markdown frontmatter (source of
-// truth; survives re-ingest / engine rebuild) AND the engine `pages.frontmatter`
-// JSONB (so the metric reflects it immediately, no re-sync needed).
-
-import { existsSync, readFileSync, writeFileSync } from 'node:fs';
-import { isAbsolute, join, resolve } from 'node:path';
-import { setCliExitVerdict } from '../core/cli-force-exit.ts';
-import type { BrainEngine } from '../core/engine.ts';
-import { REFERENCE_FRONTMATTER_KEY } from '../core/reference-flag.ts';
-import { resolveSourceId } from '../core/source-resolver.ts';
-
-/** Insert/replace/remove `reference: true` in a markdown frontmatter block.
- *  Minimal-diff: only the one line changes; key order is otherwise preserved. */
-export function applyReferenceFrontmatter(content: string, on: boolean): string {
-  const keyLine = `${REFERENCE_FRONTMATTER_KEY}: true`;
-  const block = content.match(/^---\n([\s\S]*?)\n---/);
-
-  if (!block) {
-    // No frontmatter. Nothing to remove; if setting, prepend a block.
-    if (!on) return content;
-    return `---\n${keyLine}\n---\n\n${content}`;
-  }
-
-  let fm = block[1];
-  const hasKey = new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$`, 'm').test(fm);
-
-  if (on) {
-    fm = hasKey
-      ? fm.replace(new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$`, 'm'), keyLine)
-      : `${fm}\n${keyLine}`;
-  } else {
-    if (!hasKey) return content;
-    fm = fm.replace(new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$\\n?`, 'm'), '');
-  }
-
-  // Function replacement so YAML chars ($, & …) in fm aren't treated as
-  // replacement patterns.
-  return content.replace(/^---\n[\s\S]*?\n---/, () => `---\n${fm}\n---`);
-}
-
-function parseArgs(args: string[]): { slug?: string; unset: boolean; json: boolean; brain?: string; source?: string } {
-  let slug: string | undefined;
-  let unset = false;
-  let json = false;
-  let brain: string | undefined;
-  let source: string | undefined;
-  for (let i = 0; i < args.length; i++) {
-    const a = args[i];
-    if (a === '--unset') unset = true;
-    else if (a === '--json') json = true;
-    else if (a === '--brain' || a === '--dir') brain = args[++i];
-    else if (a === '--source') source = args[++i];
-    else if (!a.startsWith('--') && !slug) slug = a;
-  }
-  return { slug, unset, json, brain, source };
-}
-
-async function resolveBrainDir(engine: BrainEngine, explicit?: string): Promise<string | null> {
-  if (explicit) return resolve(explicit);
-  const configured = await engine.getConfig('sync.repo_path');
-  if (configured && existsSync(configured)) return resolve(configured);
-  return null;
-}
-
-export async function runReference(engine: BrainEngine, args: string[]): Promise<void> {
-  const { slug, unset, json, brain, source } = parseArgs(args);
-  if (!slug) {
-    console.error('Usage: gbrain reference <slug> [--unset] [--source <id>] [--brain <dir>] [--json]');
-    setCliExitVerdict(2);
-    return;
-  }
-
-  const brainDir = await resolveBrainDir(engine, brain);
-  if (!brainDir) {
-    console.error('reference: could not resolve brain dir. Pass --brain <dir> or set sync.repo_path.');
-    setCliExitVerdict(1);
-    return;
-  }
-
-  const rel = slug.endsWith('.md') ? slug : `${slug}.md`;
-  const filePath = isAbsolute(rel) ? rel : join(brainDir, rel);
-  if (!existsSync(filePath)) {
-    console.error(`reference: page not found on disk: ${filePath}`);
-    setCliExitVerdict(1);
-    return;
-  }
-
-  // 1) Durable: edit the markdown frontmatter.
-  const before = readFileSync(filePath, 'utf8');
-  const after = applyReferenceFrontmatter(before, !unset);
-  const fileChanged = after !== before;
-  if (fileChanged) writeFileSync(filePath, after, 'utf8');
-
-  // 2) Immediate: update the engine frontmatter JSONB so the metric reflects it
-  //    without waiting for a re-sync. Scoped to (source_id, slug) — slug is only
-  //    unique per source, so a bare-slug UPDATE would clobber same-named pages
-  //    in every other source. Resolve the source from the brain dir (tier-4
-  //    local_path match) unless --source / GBRAIN_SOURCE overrides.
-  const cleanSlug = slug.replace(/\.md$/, '');
-  const sourceId = await resolveSourceId(engine, source ?? null, brainDir);
-  if (unset) {
-    await engine.executeRaw(
-      `UPDATE pages SET frontmatter = frontmatter - '${REFERENCE_FRONTMATTER_KEY}' WHERE slug = $1 AND source_id = $2`,
-      [cleanSlug, sourceId],
-    );
-  } else {
-    await engine.executeRaw(
-      `UPDATE pages SET frontmatter = jsonb_set(COALESCE(frontmatter, '{}'::jsonb), '{${REFERENCE_FRONTMATTER_KEY}}', 'true'::jsonb) WHERE slug = $1 AND source_id = $2`,
-      [cleanSlug, sourceId],
-    );
-  }
-
-  const result = { slug: cleanSlug, source_id: sourceId, reference: !unset, file_changed: fileChanged, file: filePath };
-  if (json) {
-    console.log(JSON.stringify(result));
-  } else {
-    const verb = unset ? 'unmarked' : 'marked';
-    console.log(`${verb} ${cleanSlug} as reference=${!unset}${fileChanged ? '' : ' (frontmatter already current)'}`);
-    if (!unset) {
-      console.log('  → exempt from timeline_coverage / entity_link_coverage; still fully searchable & linkable.');
-    }
-  }
-}

src/core/onboard/checks.ts

@@ -18,7 +18,6 @@
 import type { BrainEngine } from '../engine.ts';
 import type { RemediationStep } from '../remediation-step.ts';
 import { makeRemediationStep } from '../remediation-step.ts';
-import { referenceExclusionSql } from '../reference-flag.ts';
 
 /** Shared shape returned by all four checks. */
 export interface OnboardCheckResult {
@@ -121,8 +120,7 @@ export async function checkEntityLinkCoverage(
     engine,
     `SELECT COUNT(*) AS count FROM pages
        WHERE type IN ('person', 'company', 'organization', 'entity')
-         AND deleted_at IS NULL
-         AND ${referenceExclusionSql()}`,
+         AND deleted_at IS NULL`,
   );
 
   if (totalEntities === 0) {
@@ -146,7 +144,6 @@ export async function checkEntityLinkCoverage(
        SELECT p.id FROM pages p ${sampleClause}
        WHERE p.type IN ('person', 'company', 'organization', 'entity')
          AND p.deleted_at IS NULL
-         AND ${referenceExclusionSql('p')}
          AND EXISTS (SELECT 1 FROM links l WHERE l.to_page_id = p.id)
      ) sub`,
   );
@@ -218,8 +215,7 @@ export async function checkTimelineCoverage(
     engine,
     `SELECT COUNT(*) AS count FROM pages
        WHERE type IN ('person', 'company', 'organization', 'entity')
-         AND deleted_at IS NULL
-         AND ${referenceExclusionSql()}`,
+         AND deleted_at IS NULL`,
   );
 
   if (totalEntities === 0) {
@@ -241,7 +237,6 @@ export async function checkTimelineCoverage(
        SELECT p.id FROM pages p ${sampleClause}
        WHERE p.type IN ('person', 'company', 'organization', 'entity')
          AND p.deleted_at IS NULL
-         AND ${referenceExclusionSql('p')}
          AND EXISTS (SELECT 1 FROM timeline_entries t WHERE t.page_id = p.id)
      ) sub`,
   );

src/core/onboard/init-nudge.ts

@@ -14,7 +14,6 @@
 // also short-circuits (CI/scripted callers see nothing).
 
 import type { BrainEngine } from '../engine.ts';
-import { referenceExclusionSql } from '../reference-flag.ts';
 
 const NUDGE_BUDGET_MS = 3000;
 
@@ -58,8 +57,7 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
       engine.executeRaw<{ count: string | number }>(
         `SELECT COUNT(*) AS count FROM pages
            WHERE type IN ('person', 'company', 'organization', 'entity')
-             AND deleted_at IS NULL
-             AND ${referenceExclusionSql()}`,
+             AND deleted_at IS NULL`,
         [],
         { signal: controller.signal },
       ),
@@ -67,7 +65,6 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
         `SELECT COUNT(*) AS count FROM pages p
            WHERE p.type IN ('person', 'company', 'organization', 'entity')
              AND p.deleted_at IS NULL
-             AND ${referenceExclusionSql('p')}
              AND EXISTS (SELECT 1 FROM links l WHERE l.to_page_id = p.id)`,
         [],
         { signal: controller.signal },
@@ -76,7 +73,6 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
         `SELECT COUNT(*) AS count FROM pages p
            WHERE p.type IN ('person', 'company', 'organization', 'entity')
              AND p.deleted_at IS NULL
-             AND ${referenceExclusionSql('p')}
              AND EXISTS (SELECT 1 FROM timeline_entries t WHERE t.page_id = p.id)`,
         [],
         { signal: controller.signal },

src/core/operations.ts

@@ -4957,7 +4957,7 @@ const run_onboard: Operation = {
     // typo, the underlying queue.add would reject. Defense-in-depth.
     const result = await runRemediation(
       ctx.engine,
-      { targetScore, maxUsd },
+      { targetScore, maxUsd, extraRemediations: allowedExtras },
       {},
     );
 

src/core/pglite-engine.ts

@@ -23,7 +23,6 @@ import { runMigrations } from './migrate.ts';
 import { PGLITE_SCHEMA_SQL, getPGLiteSchema } from './pglite-schema.ts';
 import { DEFAULT_EMBEDDING_MODEL, DEFAULT_EMBEDDING_DIMENSIONS } from './ai/defaults.ts';
 import { DELETE_BATCH_SIZE } from './engine-constants.ts';
-import { referenceExclusionSql } from './reference-flag.ts';
 import { MARKDOWN_CHUNKER_VERSION } from './chunkers/recursive.ts';
 import { acquireLock, releaseLock, type LockHandle } from './pglite-lock.ts';
 import { getFtsLanguage } from './fts-language.ts';
@@ -5203,7 +5202,6 @@ export class PGLiteEngine implements BrainEngine {
     const { rows: [h] } = await this.db.query(`
       WITH entity_pages AS (
         SELECT id, slug FROM pages WHERE type IN ('person', 'company')
-          AND ${referenceExclusionSql()}
       )
       SELECT
         (SELECT count(*) FROM pages) as page_count,

src/core/postgres-engine.ts

@@ -5320,12 +5320,7 @@ export class PostgresEngine implements BrainEngine {
     // is working as intended, not an orphan.
     const [h] = await sql`
       WITH entity_pages AS (
-        -- reference:true pages are exempt from coverage metrics.
-        -- Inlined (postgres.js tagged-template interpolation = bound param,
-        -- not raw SQL); keep in sync with referenceExclusionSql() in
-        -- reference-flag.ts.
         SELECT id, slug FROM pages WHERE type IN ('person', 'company')
-          AND (frontmatter->>'reference') IS DISTINCT FROM 'true'
       )
       SELECT
         (SELECT count(*) FROM pages) as page_count,

src/core/reference-flag.ts

@@ -1,37 +0,0 @@
-// Reference / canon entities.
-//
-// A page with frontmatter `reference: true` is a reference-only entity — a
-// figure or organization imported from a book / article / external source that
-// the user reads ABOUT but does not actively interact with (e.g. Andy Grove,
-// Kleiner Perkins). It keeps its real `type` (`person` / `company`), so it stays
-// fully searchable, enrichable, linkable, and edge-resolvable — NOTHING about
-// retrieval changes.
-//
-// The ONLY behavior it opts out of is the entity *coverage* metrics
-// (`timeline_coverage`, `entity_link_coverage` + their onboard-nudge mirrors).
-// Those metrics nudge "this entity should accumulate dated history / inbound
-// links"; that assumption is right for people you actually deal with and wrong
-// for canon imports, which have no dated events in the user's life. Excluding
-// them keeps the metric honest and actionable instead of permanently red.
-//
-// Opt-in: absent / false / anything-but-true = normal entity (the default).
-// Set via `gbrain reference <slug>` (or hand-edit frontmatter).
-
-export const REFERENCE_FRONTMATTER_KEY = 'reference';
-
-/**
- * SQL predicate (true for NON-reference pages) to AND into entity-coverage
- * denominators AND numerators so the ratio stays consistent. JSONB `->>` yields
- * text; `IS DISTINCT FROM 'true'` treats absent (NULL) and every non-true value
- * as a normal counted entity. Backed by the GIN index on `pages.frontmatter`.
- *
- * @param alias optional table alias (e.g. 'p' for `pages p`); omit for bare `pages`.
- *
- * NOTE: postgres-engine.ts uses a postgres.js tagged template where `${}` is a
- * bound parameter, not raw SQL, so it inlines this predicate literally — keep
- * the two in sync.
- */
-export function referenceExclusionSql(alias = ''): string {
-  const col = alias ? `${alias}.frontmatter` : 'frontmatter';
-  return `(${col}->>'${REFERENCE_FRONTMATTER_KEY}') IS DISTINCT FROM 'true'`;
-}

src/core/remediation/run.ts

@@ -66,9 +66,10 @@ export async function runRemediation(
   } = await import('../remediation-checkpoint.ts');
 
   const ctx = await loadRecommendationContext(engine);
+  const extraRemediations = opts.extraRemediations ?? [];
 
   // Pre-flight ceiling check via the shared plan computation.
-  const initialPlan = await computeRemediationPlan(engine, { targetScore });
+  const initialPlan = await computeRemediationPlan(engine, { targetScore, extraRemediations });
   if (initialPlan.target_unreachable) {
     hooks.onTargetUnreachable?.(targetScore, initialPlan.max_reachable_score);
     return {
@@ -87,7 +88,7 @@ export async function runRemediation(
   }
 
   const initialHealth = await engine.getHealth();
-  let recs: RemediationStep[] = computeRecommendations(initialHealth, ctx)
+  let recs: RemediationStep[] = computeRecommendations(initialHealth, ctx, extraRemediations)
     .filter((r) => r.status === 'remediable');
   if (recs.length === 0) {
     hooks.onNothingToDo?.(initialHealth.brain_score, targetScore);
@@ -305,7 +306,13 @@ export async function runRemediation(
       // steps with bumped retry suffix (D1).
       if (recs.length === 0 || stepCount >= maxJobs) break;
       const freshHealth = await engine.getHealth();
-      recs = computeRecommendations(freshHealth, ctx).filter((r) => r.status === 'remediable');
+      // Extras carry a static status:'remediable' — a fresh health snapshot
+      // never ages them out the way health-derived steps drop. Filter out
+      // ids this run already processed (any terminal status), or the recheck
+      // would resubmit completed extras every iteration, forever.
+      const processedIds = new Set(submitted.map((s) => s.id));
+      const pendingExtras = extraRemediations.filter((r) => !processedIds.has(r.id));
+      recs = computeRecommendations(freshHealth, ctx, pendingExtras).filter((r) => r.status === 'remediable');
     }
   };
 

src/core/remediation/types.ts

@@ -63,6 +63,16 @@ export interface RemediationOpts {
   resumePlanHash?: string;
   /** Whether to attempt resume at all (default false). */
   resume?: boolean;
+  /**
+   * Caller-supplied RemediationStep entries threaded into the planner.
+   * Mirrors RemediationPlanOpts.extraRemediations so onboard's --apply
+   * --auto path (and MCP run_onboard auto modes) forward the same
+   * onboard-check remediations the --check path already passes through
+   * computeRemediationPlan. Without this the runner saw only generic
+   * brain_score remediations and reported "Nothing to do" whenever the
+   * only applicable work was an extra (e.g. extract-ner).
+   */
+  extraRemediations?: RemediationStep[];
 }
 
 /**

test/reference-flag.test.ts

@@ -1,154 +0,0 @@
-import { describe, expect, test } from 'bun:test';
-import { referenceExclusionSql, REFERENCE_FRONTMATTER_KEY } from '../src/core/reference-flag.ts';
-import { applyReferenceFrontmatter } from '../src/commands/reference.ts';
-
-describe('referenceExclusionSql', () => {
-  test('bare pages (no alias)', () => {
-    expect(referenceExclusionSql()).toBe(`(frontmatter->>'reference') IS DISTINCT FROM 'true'`);
-  });
-  test('aliased', () => {
-    expect(referenceExclusionSql('p')).toBe(`(p.frontmatter->>'reference') IS DISTINCT FROM 'true'`);
-  });
-  test('key constant', () => {
-    expect(REFERENCE_FRONTMATTER_KEY).toBe('reference');
-  });
-});
-
-describe('applyReferenceFrontmatter', () => {
-  const page = `---\ntitle: Andy Grove\ntype: person\ntags: []\n---\n\n# Andy Grove\n\nBody.`;
-
-  test('adds reference: true to an existing frontmatter block', () => {
-    const out = applyReferenceFrontmatter(page, true);
-    expect(out).toContain('reference: true');
-    expect(out).toContain('type: person');   // other keys preserved
-    expect(out).toContain('# Andy Grove');    // body preserved
-  });
-
-  test('is idempotent — does not duplicate the key', () => {
-    const once = applyReferenceFrontmatter(page, true);
-    const twice = applyReferenceFrontmatter(once, true);
-    expect(twice).toBe(once);
-    expect(twice.match(/reference: true/g)).toHaveLength(1);
-  });
-
-  test('replaces a stale reference: false with true', () => {
-    const off = `---\ntype: person\nreference: false\n---\n\nBody.`;
-    const out = applyReferenceFrontmatter(off, true);
-    expect(out).toContain('reference: true');
-    expect(out).not.toContain('reference: false');
-  });
-
-  test('--unset removes the key', () => {
-    const on = applyReferenceFrontmatter(page, true);
-    const off = applyReferenceFrontmatter(on, false);
-    expect(off).not.toContain('reference:');
-    expect(off).toContain('type: person');
-  });
-
-  test('--unset on a page without the key is a no-op', () => {
-    expect(applyReferenceFrontmatter(page, false)).toBe(page);
-  });
-
-  test('setting on a frontmatter-less page prepends a block', () => {
-    const raw = '# Just a heading\n\nNo frontmatter here.';
-    const out = applyReferenceFrontmatter(raw, true);
-    expect(out.startsWith('---\nreference: true\n---\n')).toBe(true);
-    expect(out).toContain('# Just a heading');
-  });
-
-  test('preserves body containing YAML-special chars', () => {
-    const tricky = `---\ntype: person\n---\n\nText with $& and $1 literals.`;
-    const out = applyReferenceFrontmatter(tricky, true);
-    expect(out).toContain('Text with $& and $1 literals.');
-    expect(out).toContain('reference: true');
-  });
-});
-
-// ── e2e: getHealth exemption + (source_id, slug)-scoped JSONB write ─────────
-
-import { afterAll, beforeAll } from 'bun:test';
-import * as fs from 'node:fs';
-import * as os from 'node:os';
-import * as path from 'node:path';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { runReference } from '../src/commands/reference.ts';
-import { withEnv } from './helpers/with-env.ts';
-
-describe('reference flag e2e (PGLite)', () => {
-  let engine: PGLiteEngine;
-  let brainDir: string;
-
-  beforeAll(async () => {
-    engine = new PGLiteEngine();
-    await engine.connect({ database_url: '' });
-    await engine.initSchema();
-
-    brainDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gbrain-ref-'));
-    fs.mkdirSync(path.join(brainDir, 'people'), { recursive: true });
-    fs.writeFileSync(
-      path.join(brainDir, 'people/andy-grove.md'),
-      '---\ntitle: Andy Grove\ntype: person\n---\n\n# Andy Grove\n',
-      'utf8',
-    );
-
-    await engine.executeRaw(
-      `INSERT INTO sources (id, name, local_path, config, created_at)
-       VALUES ('src-a', 'a', $1, '{}'::jsonb, now()), ('src-b', 'b', NULL, '{}'::jsonb, now())`,
-      [brainDir],
-    );
-    // Same slug in BOTH sources — the write must only touch src-a.
-    await engine.putPage('people/andy-grove', {
-      type: 'person', title: 'Andy Grove', compiled_truth: 'canon figure',
-    }, { sourceId: 'src-a' });
-    await engine.putPage('people/andy-grove', {
-      type: 'person', title: 'Andy Grove', compiled_truth: 'other-source twin',
-    }, { sourceId: 'src-b' });
-    // A normal contact WITH a timeline entry, so coverage has a live numerator.
-    const contact = await engine.putPage('people/alice-example', {
-      type: 'person', title: 'Alice Example', compiled_truth: 'real contact',
-    }, { sourceId: 'src-a' });
-    await engine.executeRaw(
-      `INSERT INTO timeline_entries (page_id, date, summary) VALUES ($1, '2026-01-01', 'met')`,
-      [contact.id],
-    );
-  });
-
-  afterAll(async () => {
-    await engine.disconnect();
-    fs.rmSync(brainDir, { recursive: true, force: true });
-  });
-
-  test('runReference scopes the JSONB write to the resolved (source_id, slug)', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () =>
-      runReference(engine, ['people/andy-grove', '--brain', brainDir]));
-
-    const rows = await engine.executeRaw<{ source_id: string; ref: string | null }>(
-      `SELECT source_id, frontmatter->>'reference' AS ref FROM pages WHERE slug = 'people/andy-grove' ORDER BY source_id`,
-    );
-    expect(rows).toEqual([
-      { source_id: 'src-a', ref: 'true' },
-      { source_id: 'src-b', ref: null },   // twin in the other source untouched
-    ]);
-    // Durable half: frontmatter on disk got the flag too.
-    expect(fs.readFileSync(path.join(brainDir, 'people/andy-grove.md'), 'utf8'))
-      .toContain('reference: true');
-  });
-
-  test('getHealth exempts reference pages from timeline/link coverage', async () => {
-    const health = await engine.getHealth();
-    // 3 person pages; the 2 reference-less twins would drag coverage to 1/3.
-    // With the src-a twin marked reference, denominator = 2 (alice + src-b twin).
-    expect(health.timeline_coverage).toBeCloseTo(0.5);
-  });
-
-  test('unset restores the page to a normal counted entity', async () => {
-    await withEnv({ GBRAIN_SOURCE: undefined }, () =>
-      runReference(engine, ['people/andy-grove', '--unset', '--brain', brainDir]));
-    const rows = await engine.executeRaw<{ ref: string | null }>(
-      `SELECT frontmatter->>'reference' AS ref FROM pages WHERE slug = 'people/andy-grove' AND source_id = 'src-a'`,
-    );
-    expect(rows[0].ref).toBeNull();
-    const health = await engine.getHealth();
-    expect(health.timeline_coverage).toBeCloseTo(1 / 3);
-  });
-});

test/remediation-run-extras.serial.test.ts

@@ -0,0 +1,108 @@
+// test/remediation-run-extras.serial.test.ts
+// Regression for PR #2161 takeover: `gbrain onboard --apply --auto` dropped
+// onboard-check extraRemediations. Two distinct halves of the bug:
+//   1. runRemediation built the pre-flight plan + initial recs WITHOUT the
+//      extras, so an extras-only plan reported "Nothing to do".
+//   2. The D7 mid-run recheck rebuilt recs WITHOUT the extras after every
+//      completed step, so with 2+ plannable steps all remaining extras were
+//      dropped after step 1. The recheck must also filter out extras this
+//      run already processed — extras carry static status:'remediable', so
+//      unfiltered threading would resubmit completed extras forever.
+//
+// SERIAL: mock.module (queue + wait-for-completion stubs, R2) + GBRAIN_HOME
+// env mutation so checkpoint files land in a tmpdir, not ~/.gbrain.
+
+import { describe, expect, test, beforeAll, afterAll, mock } from 'bun:test';
+import { mkdtempSync, rmSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { makeRemediationStep } from '../src/core/remediation-step.ts';
+
+// Stub the Minion queue: every submitted job is immediately 'completed'.
+// runRemediation only calls queue.add + waitForCompletion(queue, id).
+let nextJobId = 1;
+const submittedJobs: Array<{ name: string }> = [];
+mock.module('../src/core/minions/queue.ts', () => ({
+  MinionQueue: class {
+    async add(name: string) {
+      submittedJobs.push({ name });
+      return { id: nextJobId++, status: 'completed' };
+    }
+  },
+}));
+mock.module('../src/core/minions/wait-for-completion.ts', () => ({
+  waitForCompletion: async () => ({ status: 'completed' }),
+}));
+
+let engine: PGLiteEngine;
+let home: string;
+const prevHome = process.env.GBRAIN_HOME;
+
+beforeAll(async () => {
+  home = mkdtempSync(join(tmpdir(), 'gbrain-remextras-'));
+  process.env.GBRAIN_HOME = home;
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+}, 120_000);
+
+afterAll(async () => {
+  await engine.disconnect();
+  if (prevHome === undefined) delete process.env.GBRAIN_HOME;
+  else process.env.GBRAIN_HOME = prevHome;
+  rmSync(home, { recursive: true, force: true });
+});
+
+function extra(id: string, job: string) {
+  return makeRemediationStep({
+    id,
+    job,
+    params: {},
+    severity: 'medium',
+    est_seconds: 5,
+    est_usd_cost: 0,
+    rationale: 'synthetic onboard-check extra',
+    status: 'remediable',
+  });
+}
+
+describe('runRemediation extraRemediations threading', () => {
+  test('extras-only plan runs BOTH extras and terminates (no Nothing-to-do, no resubmit loop)', async () => {
+    // Empty PGLite brain → zero health-derived recommendations. Without the
+    // fix, half 1 makes this run return submitted: [] via onNothingToDo.
+    // With only half 1 (the original PR #2161 diff), the mid-run recheck
+    // drops the second extra after step 1 — submitted has 1 entry, not 2.
+    const { runRemediation } = await import('../src/core/remediation/run.ts');
+    let nothingToDo = false;
+    const result = await runRemediation(
+      engine,
+      {
+        targetScore: 1,
+        extraRemediations: [
+          extra('onboard.extract_ner', 'extract-ner'),
+          extra('onboard.extract_timeline', 'extract-timeline-from-meetings'),
+        ],
+        // Safety bound: an unfiltered recheck would resubmit completed
+        // extras forever; maxJobs turns that regression into a fast fail
+        // (extra count > 1 below) instead of a hung test.
+        maxJobs: 5,
+      },
+      { onNothingToDo: () => { nothingToDo = true; } },
+    );
+
+    expect(nothingToDo).toBe(false);
+    const ids = result.submitted.map((s) => s.id);
+    expect(ids).toContain('onboard.extract_ner');
+    expect(ids).toContain('onboard.extract_timeline');
+    // Each extra ran exactly once — the recheck must not re-plan extras the
+    // run already processed.
+    expect(ids.filter((i) => i === 'onboard.extract_ner').length).toBe(1);
+    expect(ids.filter((i) => i === 'onboard.extract_timeline').length).toBe(1);
+    expect(result.submitted.every((s) => s.status === 'completed')).toBe(true);
+    expect(submittedJobs.map((j) => j.name).sort()).toEqual([
+      'extract-ner',
+      'extract-timeline-from-meetings',
+    ]);
+  });
+});