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>

.github/workflows/test.yml

@@ -206,11 +206,7 @@ jobs:
     needs: cache-check
     if: needs.cache-check.outputs.hit != 'true'
     runs-on: ubuntu-latest
-    # 20 (was 15): shard 4 runs ~14.5 min on master (dream.test.ts ~29s/test
-    # dominates it) and hits the 15-min ceiling on slower runners, cancelling
-    # mid-run with 0 test failures. Rebalancing via
-    # scripts/mine-shard-weights.ts is the real fix; this stops the bleeding.
-    timeout-minutes: 20
+    timeout-minutes: 15
     strategy:
       fail-fast: false
       matrix:

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/skill-manifest.ts

@@ -23,15 +23,6 @@
  * hold conventions and shared rule files, not skills. Files like
  * `_brain-filing-rules.md` live at the root and are not considered
  * skills by either loader.
- *
- * ClawHub-installed workspace skills (#1767): a skill dir carrying
- * `.clawhub/origin.json` is an externally-managed runtime integration
- * (e.g. an email or catalog skill), not a gbrain-routable skill. The
- * derive path SKIPS those so `gbrain doctor` resolver_health doesn't
- * hard-fail on them — UNLESS the skill's SKILL.md frontmatter declares
- * `triggers:`, which is the explicit opt-in to gbrain routing (and the
- * same surface that makes it reachable). An explicit manifest.json that
- * lists a ClawHub skill also keeps strict checking (verbatim path).
  */
 
 import { existsSync, readFileSync, readdirSync, statSync } from 'fs';
@@ -69,27 +60,9 @@ function parseSkillName(skillMdPath: string): string | null {
   }
 }
 
-/**
- * Does the SKILL.md frontmatter declare a `triggers:` key? A ClawHub-
- * installed skill that ships gbrain `triggers:` has explicitly opted in
- * to gbrain routing and gets full resolver checks (#1767).
- */
-function declaresTriggers(skillMdPath: string): boolean {
-  try {
-    const content = readFileSync(skillMdPath, 'utf-8');
-    const fmMatch = content.match(/^---\n([\s\S]*?)\n---/);
-    if (!fmMatch) return false;
-    return /^triggers:/m.test(fmMatch[1]);
-  } catch {
-    return false;
-  }
-}
-
 /**
  * Walk skillsDir, return every `<skillsDir>/<dir>/SKILL.md` as a
- * ManifestEntry. Dotfile and underscore-prefixed dirs are skipped, as
- * are ClawHub-installed external skills that haven't opted in to gbrain
- * routing via `triggers:` frontmatter (#1767).
+ * ManifestEntry. Dotfile and underscore-prefixed dirs are skipped.
  */
 function deriveManifest(skillsDir: string): ManifestEntry[] {
   const out: ManifestEntry[] = [];
@@ -120,12 +93,6 @@ function deriveManifest(skillsDir: string): ManifestEntry[] {
     const skillMd = join(subdirAbs, 'SKILL.md');
     if (!existsSync(skillMd)) continue;
 
-    // ClawHub-installed external skill (#1767): skip unless it opts in
-    // to gbrain routing by declaring `triggers:` in its frontmatter.
-    if (existsSync(join(subdirAbs, '.clawhub', 'origin.json')) && !declaresTriggers(skillMd)) {
-      continue;
-    }
-
     const frontmatterName = parseSkillName(skillMd);
     const name = frontmatterName && frontmatterName !== '' ? frontmatterName : entry;
     out.push({ name, path: `${entry}/SKILL.md` });

test/check-resolvable.test.ts

@@ -382,35 +382,6 @@ describe("DRY detection — checkResolvable", () => {
   });
 });
 
-describe("#1767 — ClawHub workspace skills are not resolver-required", () => {
-  let dir: string;
-  afterEachCleanup(() => dir && rmSync(dir, { recursive: true, force: true }));
-
-  test("ClawHub skill without gbrain metadata produces no unreachable/mece_gap", () => {
-    dir = mkdtempSync(join(tmpdir(), "gbrain-clawhub-"));
-    // Native gbrain skill: routable via frontmatter triggers. No manifest.json
-    // (the OpenClaw derive path from the issue repro).
-    mkdirSync(join(dir, "query"), { recursive: true });
-    writeFileSync(
-      join(dir, "query", "SKILL.md"),
-      `---\nname: query\ndescription: test\ntriggers:\n  - "what do we know"\n---\n\n# query\n`
-    );
-    // ClawHub-installed integration: no triggers, no resolver row.
-    mkdirSync(join(dir, "agentmail", ".clawhub"), { recursive: true });
-    writeFileSync(
-      join(dir, "agentmail", ".clawhub", "origin.json"),
-      JSON.stringify({ registry: "https://clawhub.ai", slug: "agentmail" })
-    );
-    writeFileSync(join(dir, "agentmail", "SKILL.md"), `---\nname: agentmail\ndescription: email integration\n---\n\n# agentmail\n`);
-
-    const report = checkResolvable(dir);
-    const agentmailIssues = report.issues.filter(i => i.skill === "agentmail");
-    expect(agentmailIssues).toEqual([]);
-    expect(report.ok).toBe(true);
-    expect(report.summary.total_skills).toBe(1);
-  });
-});
-
 describe("v0.22.4 regression — actual repo skills/ has 0 errors", () => {
   test("repo skills/ pass check-resolvable cleanly (zero errors AND zero warnings)", () => {
     // The v0.22.4 (Part A) contract was zero warnings AND zero errors.

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/skill-manifest.test.ts

@@ -166,55 +166,6 @@ describe('loadOrDeriveManifest', () => {
     expect(r.skills.map(s => s.name)).toEqual(['apple', 'mango', 'zebra']);
   });
 
-  // #1767 — ClawHub-installed workspace skills are external integrations,
-  // not gbrain-routable skills. The derive path skips them unless they
-  // opt in via `triggers:` frontmatter.
-  it('skips ClawHub-origin skills without triggers frontmatter (#1767)', () => {
-    const dir = scratch();
-    writeSkill(dir, 'query', 'query');
-    writeSkill(dir, 'agentmail', 'agentmail');
-    mkdirSync(join(dir, 'agentmail', '.clawhub'), { recursive: true });
-    writeFileSync(
-      join(dir, 'agentmail', '.clawhub', 'origin.json'),
-      JSON.stringify({ registry: 'https://clawhub.ai', slug: 'agentmail' })
-    );
-    const r = loadOrDeriveManifest(dir);
-    expect(r.derived).toBe(true);
-    expect(r.skills.map(s => s.name)).toEqual(['query']);
-  });
-
-  it('includes ClawHub-origin skills that opt in via triggers frontmatter (#1767)', () => {
-    const dir = scratch();
-    writeSkill(dir, 'agentmail', 'agentmail');
-    mkdirSync(join(dir, 'agentmail', '.clawhub'), { recursive: true });
-    writeFileSync(
-      join(dir, 'agentmail', '.clawhub', 'origin.json'),
-      JSON.stringify({ registry: 'https://clawhub.ai', slug: 'agentmail' })
-    );
-    writeFileSync(
-      join(dir, 'agentmail', 'SKILL.md'),
-      `---\nname: agentmail\ndescription: test\ntriggers:\n  - "send email"\n---\n\n# agentmail\n`
-    );
-    const r = loadOrDeriveManifest(dir);
-    expect(r.derived).toBe(true);
-    expect(r.skills.map(s => s.name)).toEqual(['agentmail']);
-  });
-
-  it('keeps ClawHub-origin skills listed in an explicit manifest.json (#1767)', () => {
-    // Explicit manifest.json is a deliberate declaration — strict checking stays.
-    const dir = scratch();
-    writeSkill(dir, 'agentmail', 'agentmail');
-    mkdirSync(join(dir, 'agentmail', '.clawhub'), { recursive: true });
-    writeFileSync(
-      join(dir, 'agentmail', '.clawhub', 'origin.json'),
-      JSON.stringify({ registry: 'https://clawhub.ai', slug: 'agentmail' })
-    );
-    writeManifest(dir, { skills: [{ name: 'agentmail', path: 'agentmail/SKILL.md' }] });
-    const r = loadOrDeriveManifest(dir);
-    expect(r.derived).toBe(false);
-    expect(r.skills.map(s => s.name)).toEqual(['agentmail']);
-  });
-
   it('treats dirs without SKILL.md as not-a-skill', () => {
     const dir = scratch();
     writeSkill(dir, 'query', 'query');