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>

docs/tutorials/improving-skills-with-skillopt.md

@@ -233,14 +233,13 @@ keep it or `git checkout` to throw it away. Nothing is committed for you.
 
 **For a skill that ships with gbrain** (anything under the gbrain repo's own
 `skills/`): SkillOpt refuses to overwrite it by default and writes the winner to
-`skills/<name>/skillopt/proposed.md` instead (while keeping `best.md` as the
-optimizer's current-best pointer), so an optimization pass can never silently
-mutate a skill other people depend on. Two ways to handle that:
+`skills/<name>/skillopt/best.md` instead, so an optimization pass can never
+silently mutate a skill other people depend on. Two ways to handle that:
 
 ```bash
 # See the proposed improvement without touching SKILL.md (works for ANY skill):
 gbrain skillopt meeting-prep --split 1:1:1 --no-mutate
-# → writes skills/meeting-prep/skillopt/proposed.md, updates best.md, and prints the proposal path.
+# → writes skills/meeting-prep/skillopt/best.md (the proposed rewrite), prints its path. Copy what you want.
 
 # Actually rewrite a bundled skill (explicit opt-in + an independent held-out set):
 gbrain skillopt brain-ops --split 1:1:1 --allow-mutate-bundled \

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/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[];
 }
 
 /**

src/core/skillopt/orchestrator.ts

@@ -93,13 +93,7 @@ import { resolveLrSchedule } from './lr-schedule.ts';
 import { preflight, formatPreflightReport } from './preflight.ts';
 import { isRejected, loadRejectedBuffer, makeRejectedEntry, saveRejectedBuffer } from './rejected-buffer.ts';
 import { runReflect, runOneShotRewrite, describeJudges } from './reflect.ts';
-import {
-  acceptCandidate,
-  proposedPath as proposedFilePath,
-  revertAllPending,
-  skillPath,
-  writeProposed,
-} from './version-store.ts';
+import { acceptCandidate, bestPath, revertAllPending, skillPath, writeProposed } from './version-store.ts';
 import { runValidationGate, scoreSkillOnTasks } from './validate-gate.ts';
 import { ROLLOUT_SUCCESS_THRESHOLD } from './types.ts';
 import type { SkillOptOpts, EditOp, RunReceipt, BenchmarkTask } from './types.ts';
@@ -708,9 +702,9 @@ async function runOptimizationLoop(
   // to the catch's assignment values only (it can't prove the async callback ran).
   const finalOutcome = outcome as 'accepted' | 'no_improvement' | 'aborted' | 'errored';
   if (!mutateDecision.mutate && finalOutcome === 'accepted') {
-    // writeProposed() emitted both the best pointer and the stable review
-    // artifact in the accept branch. SKILL.md remains untouched.
-    proposedPath = proposedFilePath(skillsDir, skillName);
+    // best.md was written by writeProposed() in the accept branch (no-mutate
+    // path); it doubles as proposed.md for human review. SKILL.md untouched.
+    proposedPath = bestPath(skillsDir, skillName);
   } else if (mutateDecision.mutate) {
     mutatedSkillFile = finalOutcome === 'accepted';
   }

src/core/skillopt/version-store.ts

@@ -23,7 +23,6 @@
  *
  *   history.json
  *   best.md
- *   proposed.md
  *   versions/
  *     v0001_e1_s1.md
  *     v0002_e1_s2.md
@@ -53,10 +52,6 @@ export function bestPath(skillsDir: string, skillName: string): string {
   return path.join(skilloptDir(skillsDir, skillName), 'best.md');
 }
 
-export function proposedPath(skillsDir: string, skillName: string): string {
-  return path.join(skilloptDir(skillsDir, skillName), 'proposed.md');
-}
-
 export function skillPath(skillsDir: string, skillName: string): string {
   return path.join(skillsDir, skillName, 'SKILL.md');
 }
@@ -176,18 +171,17 @@ export function acceptCandidate(input: AcceptInput): AcceptResult {
 }
 
 /**
- * Write the candidate to both `best.md` and `proposed.md` WITHOUT touching
- * SKILL.md or the history ledger. `best.md` remains the optimizer's current
- * best pointer; `proposed.md` is the stable human-review artifact promised by
- * `--no-mutate`. Returns the proposal path. Each write is atomic (.tmp + rename).
+ * Write the candidate to `best.md` (which doubles as `proposed.md`) WITHOUT
+ * touching SKILL.md or the history ledger. Used by the `--no-mutate` /
+ * bundled-without-allow paths: the optimizer found a better candidate but the
+ * caller opted out of in-place mutation, so we surface it for human review.
+ * Returns the path written. Atomic (.tmp + rename).
  */
 export function writeProposed(skillsDir: string, skillName: string, candidateText: string): string {
-  const best = bestPath(skillsDir, skillName);
-  const proposed = proposedPath(skillsDir, skillName);
-  fs.mkdirSync(path.dirname(best), { recursive: true });
-  atomicWrite(best, candidateText);
-  atomicWrite(proposed, candidateText);
-  return proposed;
+  const p = bestPath(skillsDir, skillName);
+  fs.mkdirSync(path.dirname(p), { recursive: true });
+  atomicWrite(p, candidateText);
+  return p;
 }
 
 /**

test/e2e/skillopt-loop.serial.test.ts

@@ -39,7 +39,6 @@ import { runSkillOpt } from '../../src/core/skillopt/orchestrator.ts';
 import {
   bestPath,
   loadHistory,
-  proposedPath,
   skillPath,
 } from '../../src/core/skillopt/version-store.ts';
 import { loadRejectedBuffer } from '../../src/core/skillopt/rejected-buffer.ts';
@@ -742,7 +741,7 @@ describe('skillopt T3 — F11 held-out gate, ablation opts, no-DB-pollution', ()
     } finally { fixture.cleanup(); }
   });
 
-  test('--no-mutate writes proposed.md and best.md, leaves SKILL.md untouched', async () => {
+  test('--no-mutate writes proposed.md (best.md), leaves SKILL.md untouched', async () => {
     const fixture = setupFixture(SKILL_PEOPLE_ONLY, CITATIONS_BENCHMARK);
     try {
       installStub({
@@ -754,9 +753,10 @@ describe('skillopt T3 — F11 held-out gate, ablation opts, no-DB-pollution', ()
           const result = await runOnce(fixture, { noMutate: true });
           expect(result.outcome).toBe('accepted');
           expect(result.mutatedSkillFile).toBe(false);
-          expect(result.proposedPath).toBe(proposedPath(fixture.skillsDir, SKILL));
+          expect(result.proposedPath).toBeDefined();
+          // proposed.md (best.md) exists and carries the improvement.
+          expect(fs.existsSync(result.proposedPath!)).toBe(true);
           expect(fs.readFileSync(result.proposedPath!, 'utf8')).toContain('## Citations');
-          expect(fs.readFileSync(bestPath(fixture.skillsDir, SKILL), 'utf8')).toContain('## Citations');
           // SKILL.md on disk is UNCHANGED (still People-only).
           const skill = fs.readFileSync(skillPath(fixture.skillsDir, SKILL), 'utf8');
           expect(skill).not.toContain('## Citations');

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

test/skillopt/version-store.test.ts

@@ -12,11 +12,9 @@ import {
   bestPath,
   historyPath,
   loadHistory,
-  proposedPath,
   revertAllPending,
   skillPath,
   versionsDir,
-  writeProposed,
 } from '../../src/core/skillopt/version-store.ts';
 
 let tmpDir: string;
@@ -81,19 +79,6 @@ describe('acceptCandidate (D8 two-phase commit)', () => {
   });
 });
 
-describe('writeProposed', () => {
-  test('writes distinct best and proposed artifacts without mutating SKILL.md (#2635)', () => {
-    const candidate = '---\nname: test\n---\nproposed body\n';
-
-    const written = writeProposed(tmpDir, SKILL, candidate);
-
-    expect(written).toBe(proposedPath(tmpDir, SKILL));
-    expect(fs.readFileSync(bestPath(tmpDir, SKILL), 'utf8')).toBe(candidate);
-    expect(fs.readFileSync(proposedPath(tmpDir, SKILL), 'utf8')).toBe(candidate);
-    expect(fs.readFileSync(skillPath(tmpDir, SKILL), 'utf8')).toContain('baseline body');
-  });
-});
-
 describe('revertAllPending (D8 crash recovery)', () => {
   test('no-op when no pending rows', () => {
     const reverted = revertAllPending(tmpDir, SKILL);