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>

src/commands/extract.ts

@@ -509,12 +509,8 @@ export function extractTimelineFromContent(content: string, slug: string): Extra
   // DB-level uniqueness cannot collapse.
   const citationPattern = /\[Source:\s*([^\]]+?),\s*(\d{4}-\d{2}-\d{2})\s*\]/g;
   const bulletLinePattern = /^-\s+\*\*\d{4}-\d{2}-\d{2}\*\*\s*\|/;
-  // Lines captured by Format 4 (plain bullet) are skipped for the same
-  // reason: quality.md mandates a trailing [Source: ...] on those bullets,
-  // and re-extracting the citation would double-count the event.
-  const plainBulletLinePattern = /^-\s+\d{4}-\d{2}-\d{2}\s*[—–-]/;
   for (const line of content.split(/\r?\n/)) {
-    if (bulletLinePattern.test(line) || plainBulletLinePattern.test(line)) continue;
+    if (bulletLinePattern.test(line)) continue;
     const lineMatches = [...line.matchAll(citationPattern)];
     if (lineMatches.length === 0) continue;
     // Strip every citation marker from the line to leave the annotated text.
@@ -530,19 +526,6 @@ export function extractTimelineFromContent(content: string, slug: string): Extra
     }
   }
 
-  // Format 4: Plain bullet — - YYYY-MM-DD — Summary
-  // This is the format gbrain's own enrich skill writes (no bold, no source
-  // pipe). Without it, every brain-authored timeline entry is invisible to
-  // extraction and timeline_coverage stays at 0%. Anchored at line start so a
-  // date inside a summary/link cannot start a spurious entry; a bold Format-1
-  // line (`- **…**`) cannot match here (a `*` follows the bullet, not a
-  // digit), and the citation loop above skips these lines, so a plain bullet
-  // carrying its own [Source: ...] files exactly one entry.
-  const plainBulletPattern = /^-\s+(\d{4}-\d{2}-\d{2})\s*[—–-]\s*(.+)$/gm;
-  while ((match = plainBulletPattern.exec(content)) !== null) {
-    entries.push({ slug, date: match[1], source: 'markdown', summary: match[2].trim() });
-  }
-
   return entries;
 }
 

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/core/link-extraction.ts

@@ -1103,11 +1103,6 @@ export interface TimelineCandidate {
 // Match: `- **YYYY-MM-DD** | summary` or `- **YYYY-MM-DD** -- summary`
 // or `- **YYYY-MM-DD** - summary` or just `**YYYY-MM-DD** | summary`.
 const TIMELINE_LINE_RE = /^\s*-?\s*\*\*(\d{4}-\d{2}-\d{2})\*\*\s*[|\-–—]+\s*(.+?)\s*$/;
-// Plain bullet: `- YYYY-MM-DD — summary` (no bold, no source pipe). Kept in
-// sync with extractTimelineFromContent's Format 4 (the fs-source path).
-// Anchored flush-left so a date inside an indented continuation line cannot
-// start a spurious entry.
-const PLAIN_TIMELINE_LINE_RE = /^-\s+(\d{4}-\d{2}-\d{2})\s*[—–-]\s*(.+?)\s*$/;
 
 /**
  * Parse timeline entries from content. Looks at:
@@ -1124,7 +1119,7 @@ export function parseTimelineEntries(content: string): TimelineCandidate[] {
 
   let i = 0;
   while (i < lines.length) {
-    const m = TIMELINE_LINE_RE.exec(lines[i]) ?? PLAIN_TIMELINE_LINE_RE.exec(lines[i]);
+    const m = TIMELINE_LINE_RE.exec(lines[i]);
     if (!m) {
       i++;
       continue;
@@ -1141,7 +1136,7 @@ export function parseTimelineEntries(content: string): TimelineCandidate[] {
     let j = i + 1;
     while (j < lines.length) {
       const next = lines[j];
-      if (TIMELINE_LINE_RE.test(next) || PLAIN_TIMELINE_LINE_RE.test(next)) break;
+      if (TIMELINE_LINE_RE.test(next)) break;
       if (/^#{1,6}\s/.test(next)) break;
       if (next.trim().length === 0 && detailLines.length === 0) {
         // skip leading blank line; if we hit a blank after detail content
@@ -1171,7 +1166,7 @@ export function parseTimelineEntries(content: string): TimelineCandidate[] {
   // bullet pass are skipped (a bullet often carries its own citation).
   const citationRe = /\[Source:\s*([^\]]+?),\s*(\d{4}-\d{2}-\d{2})\s*\]/g;
   for (const line of lines) {
-    if (TIMELINE_LINE_RE.test(line) || PLAIN_TIMELINE_LINE_RE.test(line)) continue;
+    if (TIMELINE_LINE_RE.test(line)) continue;
     const matches = [...line.matchAll(citationRe)];
     if (matches.length === 0) continue;
     const summary = line

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/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/extract.test.ts

@@ -185,49 +185,6 @@ describe('extractTimelineFromContent', () => {
     expect(entries).toHaveLength(1);
     expect(entries[0].summary).toBe('Landed the enterprise pilot with acme-example.');
   });
-
-  // Format 4: the plain bullet `- YYYY-MM-DD — Summary` that gbrain's own
-  // enrich skill writes. Before this was supported, every brain-authored
-  // timeline entry was invisible and timeline_coverage was stuck at 0%.
-  it('extracts plain bullet format (- YYYY-MM-DD — Summary)', () => {
-    const content = `## Timeline\n- 2026-06-01 — Catch-up call with alice-example; intros offered.`;
-    const entries = extractTimelineFromContent(content, 'people/alice-example');
-    expect(entries).toHaveLength(1);
-    expect(entries[0].date).toBe('2026-06-01');
-    expect(entries[0].source).toBe('markdown');
-    expect(entries[0].summary).toBe('Catch-up call with alice-example; intros offered.');
-  });
-
-  it('files exactly one entry for a plain bullet that carries its own citation', () => {
-    // quality.md mandates this shape; it must not double-count via the
-    // citation arm (Format 3) AND the plain-bullet arm (Format 4).
-    const content = `- 2026-05-31 — Confirmed full name. [Source: User, 2026-05-31]`;
-    const entries = extractTimelineFromContent(content, 'people/charlie-example');
-    expect(entries).toHaveLength(1);
-    expect(entries[0].date).toBe('2026-05-31');
-    expect(entries[0].source).toBe('markdown');
-    expect(entries[0].summary).toContain('Confirmed full name.');
-  });
-
-  it('does not double-count bold (Format 1) lines as plain bullets', () => {
-    const content = `- **2025-03-18** | Meeting — Discussed partnership`;
-    const entries = extractTimelineFromContent(content, 'test');
-    expect(entries).toHaveLength(1);
-    expect(entries[0].source).toBe('Meeting');
-  });
-
-  it('does not start a spurious entry from a date inside a summary', () => {
-    const content = `- 2026-06-01 — See [meeting](meetings/2026-06-01).`;
-    const entries = extractTimelineFromContent(content, 'people/alice-example');
-    expect(entries).toHaveLength(1);
-    expect(entries[0].date).toBe('2026-06-01');
-  });
-
-  it('handles en dash and hyphen separators in plain bullets', () => {
-    const content = `- 2026-06-01 – First\n- 2026-06-02 - Second`;
-    const entries = extractTimelineFromContent(content, 'test');
-    expect(entries).toHaveLength(2);
-  });
 });
 
 describe('walkMarkdownFiles', () => {

test/link-extraction.test.ts

@@ -720,30 +720,6 @@ More prose here.
     const entries = parseTimelineEntries(content);
     expect(entries.length).toBe(2);
   });
-
-  // Plain bullet (extract.ts Format 4 parity — the db-source path must see
-  // the same entries as the fs-source path).
-  test('parses plain bullet: - YYYY-MM-DD — summary', () => {
-    const entries = parseTimelineEntries('## Timeline\n- 2026-06-01 — Catch-up call with alice-example');
-    expect(entries.length).toBe(1);
-    expect(entries[0].date).toBe('2026-06-01');
-    expect(entries[0].summary).toBe('Catch-up call with alice-example');
-  });
-
-  test('files exactly one entry for a plain bullet carrying its own citation', () => {
-    const entries = parseTimelineEntries('- 2026-05-31 — Confirmed full name. [Source: User, 2026-05-31]');
-    expect(entries.length).toBe(1);
-    expect(entries[0].date).toBe('2026-05-31');
-  });
-
-  test('skips invalid dates in plain bullets', () => {
-    expect(parseTimelineEntries('- 2026-13-45 — Bad date').length).toBe(0);
-  });
-
-  test('does not double-count a bold bullet as a plain bullet', () => {
-    const entries = parseTimelineEntries('- **2026-01-15** | Met with Alice');
-    expect(entries.length).toBe(1);
-  });
 });
 
 // ─── isAutoLinkEnabled ─────────────────────────────────────────

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',
+    ]);
+  });
+});