fix(test): quarantine remediation-run-loop test as serial + complete BrainHealth fixture

Two CI failures, one root cause each:
- verify (check:test-isolation + typecheck): the new test uses mock.module
  (R2) so it must live in the *.serial.test.ts quarantine, and the
  BrainHealth fixture was missing the now-required linkable_page_count.
- test (6): the top-level mock.module('../src/core/ai/gateway.ts') leaked
  into other files in the parallel shard process, flaking
  test/ai/adaptive-embed-batch.test.ts. Serial quarantine fixes it —
  run-serial-tests.sh executes each serial file in its own bun process.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/core/remediation/run.ts

@@ -183,6 +183,7 @@ export async function runRemediation(
   // Real submission path
   const submitted: StepResult[] = [];
   const abortedIds = new Set<string>();
+  const attemptedIds = new Set<string>();
   const doctorRunId = crypto.randomUUID();
 
   const { MinionQueue } = await import('../minions/queue.ts');
@@ -232,6 +233,7 @@ export async function runRemediation(
       if (completedFromCheckpoint.has(step.id)) {
         const result: StepResult = { step: stepCount, id: step.id, job_id: null, status: 'completed' };
         submitted.push(result);
+        attemptedIds.add(step.id);
         hooks.onStepEnd?.(result);
         recs.shift();
         continue;
@@ -242,6 +244,7 @@ export async function runRemediation(
         const result: StepResult = { step: stepCount, id: step.id, job_id: null, status: 'skipped_dep_aborted' };
         submitted.push(result);
         abortedIds.add(step.id);
+        attemptedIds.add(step.id);
         hooks.onStepEnd?.(result);
         recs.shift();
         continue;
@@ -300,19 +303,22 @@ export async function runRemediation(
         hooks.onStepEnd?.(errResult);
       }
 
+      attemptedIds.add(step.id);
       recs.shift();
       // D7: scoped recheck — re-compute plan from fresh health snapshot.
-      // The next plan may drop completed steps and re-introduce failed
-      // steps with bumped retry suffix (D1).
+      // Queue-level max_attempts handles retries within a submitted attempt.
+      // A stuck health signal regenerates the same stable id, so keep ids this
+      // run already attempted out of the refreshed list to avoid re-enqueueing
+      // them forever.
       if (recs.length === 0 || stepCount >= maxJobs) break;
       const freshHealth = await engine.getHealth();
       // 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');
+      const pendingExtras = extraRemediations.filter((r) => !attemptedIds.has(r.id));
+      recs = computeRecommendations(freshHealth, ctx, pendingExtras)
+        .filter((r) => r.status === 'remediable' && !attemptedIds.has(r.id));
     }
   };
 
@@ -329,8 +335,8 @@ export async function runRemediation(
   }
 
   // Clear checkpoint on a clean run (no budget abort). Failed steps in the
-  // submitted set don't disqualify the cleanup — they re-surface on the
-  // next plan with bumped suffixes.
+  // submitted set don't disqualify cleanup; an uncleared health signal can
+  // produce the same stable id again in a later run.
   if (!budgetAbort) {
     clearRemediationCheckpoint(planHash);
   }

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

@@ -0,0 +1,80 @@
+import { describe, expect, mock, test } from 'bun:test';
+import type { BrainEngine } from '../src/core/engine.ts';
+import type { BrainHealth } from '../src/core/types.ts';
+
+const attemptedJobs: string[] = [];
+
+mock.module('../src/core/minions/queue.ts', () => ({
+  MinionQueue: class {
+    async add(name: string) {
+      attemptedJobs.push(name);
+      return { id: attemptedJobs.length };
+    }
+  },
+}));
+
+mock.module('../src/core/minions/wait-for-completion.ts', () => ({
+  waitForCompletion: async (_queue: unknown, jobId: number) => ({
+    id: jobId,
+    status: 'completed',
+  }),
+}));
+
+mock.module('../src/core/remediation-checkpoint.ts', () => ({
+  computePlanHash: (ids: string[]) => [...ids].sort().join('|'),
+  saveRemediationCheckpoint: () => undefined,
+  loadRemediationCheckpoint: () => null,
+  listRemediationCheckpoints: () => [],
+  clearRemediationCheckpoint: () => undefined,
+}));
+
+mock.module('../src/core/ai/gateway.ts', () => ({
+  getEmbeddingModel: () => 'ollama:nomic-embed-text',
+  getEmbeddingDimensions: () => 768,
+  withBudgetTracker: async (_tracker: unknown, fn: () => Promise<void>) => fn(),
+}));
+
+const { runRemediation } = await import('../src/core/remediation/run.ts');
+
+function makeHealth(): BrainHealth {
+  return {
+    page_count: 100,
+    linkable_page_count: 100,
+    embed_coverage: 1,
+    stale_pages: 1,
+    orphan_pages: 0,
+    missing_embeddings: 0,
+    brain_score: 80,
+    dead_links: 1,
+    link_coverage: 1,
+    timeline_coverage: 1,
+    most_connected: [],
+    embed_coverage_score: 35,
+    link_density_score: 25,
+    timeline_coverage_score: 15,
+    no_orphans_score: 15,
+    no_dead_links_score: 0,
+  };
+}
+
+describe('runRemediation recheck loop guard', () => {
+  test('attempts a stable stuck remediation once and continues to later work', async () => {
+    attemptedJobs.length = 0;
+    const health = makeHealth();
+    const engine = {
+      kind: 'postgres',
+      getHealth: async () => health,
+      getConfig: async (key: string) => key === 'sync.repo_path' ? '/brain' : null,
+    } as BrainEngine;
+
+    const result = await runRemediation(engine, { maxJobs: 4 });
+
+    expect(attemptedJobs.filter((name) => name === 'backlinks')).toHaveLength(1);
+    expect(attemptedJobs).toEqual(['backlinks', 'sync', 'extract']);
+    expect(result.submitted.map((step) => step.id)).toEqual([
+      'backlinks.fix',
+      'sync.repo',
+      'extract.all',
+    ]);
+  });
+});