fix(sync): guard putPage 0-row RETURNING + reclassify sync failure copy (#2189)

Root cause of #2189's opaque per-file crash: putPage's INSERT … ON CONFLICT
DO UPDATE … RETURNING can yield 0 rows when brain-local DB state (e.g. a
BEFORE trigger) suppresses the write, and rowToPage(rows[0]) then died with
"undefined is not an object (evaluating 'row.deleted_at')". Both engines now
throw a descriptive error naming the slug + source_id so the failure is
diagnosable per-file instead of an anonymous TypeError.

Also lands the salvageable parts of community PR #2586 (takeover): the
"failed to parse / fix the frontmatter" copy misclassified runtime import
errors as YAML problems — reworded to "failed to import" — plus its
first-code-sync PGLite smoke test.

New regression test reproduces the exact 0-row RETURNING state via a
suppressing trigger: fails pre-fix with the reported crash signature,
passes with the guard.

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

src/commands/autopilot.ts

@@ -686,7 +686,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
       try {
         const { MinionQueue } = await import('../core/minions/queue.ts');
         const { computeRecommendations, embeddingProviderConfigured, HOSTED_EMBED_KEY_CONFIG } = await import('../core/brain-score-recommendations.ts');
-        const { countExtractionLag } = await import('../core/remediation/context.ts');
         const queue = new MinionQueue(engine);
         const slotMs = Math.floor(Date.now() / (baseInterval * 1000)) * baseInterval * 1000;
         const slot = new Date(slotMs).toISOString();
@@ -878,9 +877,6 @@ export async function runAutopilot(engine: BrainEngine, args: string[]) {
             return !!(process.env[envVar] || (cfgField ? embedKeyCfg[cfgField] : undefined));
           }),
           hasChatApiKey: !!(process.env.ANTHROPIC_API_KEY || await engine.getConfig('anthropic_api_key')),
-          // Real extraction-lag gate for sync.repo/extract.all — same counter
-          // loadRecommendationContext uses (replaces the health.stale_pages proxy).
-          extractionLagPages: await countExtractionLag(engine),
         };
         // v0.41.18.0 (A5 + A19 + A22, T15): consult onboard recommendations
         // ALONGSIDE doctor's brain-score recommendations. Onboard's 4 new

src/commands/sync.ts

@@ -197,7 +197,7 @@ export interface SyncResult {
   /** Pages re-embedded during this sync's auto-embed step. 0 if --no-embed or skipped. */
   embedded: number;
   pagesAffected: string[];
-  failedFiles?: number; // count of parse failures (Bug 9)
+  failedFiles?: number; // count of per-file import/sync failures (Bug 9)
   /**
    * v0.41.13.0 partial-sync fields (only set when status === 'partial').
    *
@@ -3183,7 +3183,7 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
     await clearOpCheckpoint(engine, ckpt.target);
   };
 
-  // issue #1939 adversarial finding #1: a file that failed to parse (open ledger
+  // issue #1939 adversarial finding #1: a file that failed to import (open ledger
   // row) and is then deleted/renamed-away never re-enters failedFiles and never
   // imports, so its row would never clear and would age doctor to a permanent
   // FAIL. Treat removed paths as resolved so the ledger self-heals.
@@ -3215,9 +3215,9 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
     } else {
       const fileFailCount = failedFiles.filter(f => isSkippablePath(f.path)).length;
       serr(
-        `\nSync blocked: ${fileFailCount} file(s) failed to parse:\n` +
+        `\nSync blocked: ${fileFailCount} file(s) failed to import:\n` +
         `${codeBreakdown}\n\n` +
-        `Fix the frontmatter and re-run, or use 'gbrain sync --skip-failed' to ` +
+        `Fix the listed file errors and re-run, or use 'gbrain sync --skip-failed' to ` +
         `acknowledge and move on. A file that keeps failing auto-skips after ` +
         `${resolveAutoSkipThreshold()} consecutive syncs.`,
       );
@@ -5355,7 +5355,7 @@ function printSyncResult(result: SyncResult, sink: NodeJS.WriteStream = process.
     case 'dry_run':
       break; // already printed in performSync
     case 'blocked_by_failures':
-      write(`Sync BLOCKED at ${result.toCommit.slice(0, 8)}: ${result.failedFiles ?? 0} file(s) failed to parse.`);
+      write(`Sync BLOCKED at ${result.toCommit.slice(0, 8)}: ${result.failedFiles ?? 0} file(s) failed to import.`);
       write(`  See ~/.gbrain/sync-failures.jsonl for details, or run 'gbrain doctor'.`);
       write(`  Fix the files then re-run 'gbrain sync', or 'gbrain sync --skip-failed' to move on.`);
       break;

src/core/brain-score-recommendations.ts

@@ -146,16 +146,6 @@ export interface RecommendationContext {
   chatModel?: string;
   /** Whether the chat provider has a usable API key. */
   hasChatApiKey?: boolean;
-  /**
-   * Count of pages needing link/timeline extraction — the SAME staleness the
-   * `gbrain extract --stale` walk and doctor's `links_extraction_lag` check use
-   * (`engine.countStalePagesForExtraction`). Gates the sync→extract pipeline
-   * (sync.repo / extract.all). Replaces the old `health.stale_pages` gate, which
-   * counted "pages whose updated_at predates their newest timeline entry" — a
-   * proxy that broke when the updated_at-on-timeline-insert trigger was dropped
-   * (migration v10) and never reflected real extraction work.
-   */
-  extractionLagPages?: number;
 }
 
 /** Triage result for one check. */
@@ -202,28 +192,20 @@ export function computeRecommendations(
   const source = ctx.sourceId ?? 'default';
 
   // ---------------------------------------------------------------------
-  // sync.repo + extract.all — the materialization pipeline, gated on the REAL
-  // extraction lag (pages whose link/timeline edges are stale), NOT on the
-  // legacy `health.stale_pages` proxy. `extractionLagPages` comes from the same
-  // counter the `extract --stale` walk + doctor's `links_extraction_lag` use, so
-  // the recommendation can only fire when running extract will actually reduce
-  // it (and clear the rec). See RecommendationContext.extractionLagPages.
-  // sync.repo is the prerequisite: re-sync so pages are current before extract
-  // materializes their edges.
+  // sync.repo — fires when sync hasn't run recently OR pages are stale
   // ---------------------------------------------------------------------
-  const extractionLag = ctx.extractionLagPages ?? 0;
-  if (ctx.repoPath && extractionLag > 0) {
+  if (ctx.repoPath && health.stale_pages > 0) {
     const params = { repoPath: ctx.repoPath, sourceId: ctx.sourceId, noEmbed: true };
     out.push({
       id: 'sync.repo',
       job: 'sync',
       params,
       idempotency_key: idemKey(source, 'sync', params),
-      severity: extractionLag > 50 ? 'high' : 'medium',
-      est_seconds: Math.min(600, 30 + extractionLag * 0.5),
+      severity: health.stale_pages > 50 ? 'high' : 'medium',
+      est_seconds: Math.min(600, 30 + health.stale_pages * 0.5),
       est_usd_cost: 0,  // sync is fs+DB only
       depends_on: [],
-      rationale: `Sync before extracting ${extractionLag} page${extractionLag === 1 ? '' : 's'} with stale link/timeline edges`,
+      rationale: `${health.stale_pages} stale page${health.stale_pages === 1 ? '' : 's'} on disk`,
       status: 'remediable',
     });
   }
@@ -255,7 +237,7 @@ export function computeRecommendations(
       est_seconds: Math.min(3600, 5 + health.missing_embeddings * 0.05),
       est_usd_cost,
       // sync should run first so embed sees fresh pages.
-      depends_on: ctx.repoPath && extractionLag > 0 ? ['sync.repo'] : [],
+      depends_on: ctx.repoPath && health.stale_pages > 0 ? ['sync.repo'] : [],
       rationale: `${health.missing_embeddings} chunk${health.missing_embeddings === 1 ? '' : 's'} invisible to vector search`,
       status: 'remediable',
     });
@@ -285,7 +267,7 @@ export function computeRecommendations(
   // Triggered when sync.repo fires (because sync was set to noEmbed:true,
   // and noExtract:true after T5 lands → extract job is the materializer).
   // ---------------------------------------------------------------------
-  if (ctx.repoPath && extractionLag > 0) {
+  if (ctx.repoPath && health.stale_pages > 0) {
     const params = { mode: 'all', dir: ctx.repoPath };
     out.push({
       id: 'extract.all',
@@ -296,7 +278,7 @@ export function computeRecommendations(
       est_seconds: Math.min(600, 30 + health.page_count * 0.01),
       est_usd_cost: 0,
       depends_on: ['sync.repo'],
-      rationale: `Materialize link + timeline edges for ${extractionLag} page${extractionLag === 1 ? '' : 's'} with stale extraction`,
+      rationale: 'Materialize link + timeline edges from fresh pages',
       status: 'remediable',
     });
   }

src/core/pglite-engine.ts

@@ -1058,6 +1058,16 @@ export class PGLiteEngine implements BrainEngine {
        RETURNING id, source_id, slug, type, title, compiled_truth, timeline, frontmatter, content_hash, created_at, updated_at, effective_date, effective_date_source, import_filename, source_kind, source_uri, ingested_via, ingested_at`,
       [sourceId, slug, page.type, pageKind, page.title, page.compiled_truth, page.timeline || '', JSON.stringify(frontmatter), hash, effectiveDate, effectiveDateSource, importFilename, chunkerVersion, sourcePath, sourceKind, sourceUri, ingestedVia, ingestedAt]
     );
+    // #2189: an INSERT … ON CONFLICT DO UPDATE … RETURNING that yields 0 rows
+    // (e.g. a BEFORE trigger suppressing the write) previously crashed in
+    // rowToPage with an opaque "undefined is not an object (row.deleted_at)".
+    // Throw a diagnosable error naming the row instead. Mirrors postgres-engine.ts.
+    if (!rows[0]) {
+      throw new Error(
+        `putPage: INSERT … RETURNING produced no row for slug='${slug}' source_id='${sourceId}'. ` +
+        `A trigger or rule on the pages table may be suppressing the write.`
+      );
+    }
     return rowToPage(rows[0] as Record<string, unknown>);
   }
 

src/core/postgres-engine.ts

@@ -1119,6 +1119,16 @@ export class PostgresEngine implements BrainEngine {
         ingested_at           = COALESCE(EXCLUDED.ingested_at,           pages.ingested_at)
       RETURNING id, source_id, slug, type, title, compiled_truth, timeline, frontmatter, content_hash, created_at, updated_at, effective_date, effective_date_source, import_filename, source_kind, source_uri, ingested_via, ingested_at
     `;
+    // #2189: an INSERT … ON CONFLICT DO UPDATE … RETURNING that yields 0 rows
+    // (e.g. a BEFORE trigger suppressing the write) previously crashed in
+    // rowToPage with an opaque "undefined is not an object (row.deleted_at)".
+    // Throw a diagnosable error naming the row instead. Mirrors pglite-engine.ts.
+    if (!rows[0]) {
+      throw new Error(
+        `putPage: INSERT … RETURNING produced no row for slug='${slug}' source_id='${sourceId}'. ` +
+        `A trigger or rule on the pages table may be suppressing the write.`
+      );
+    }
     return rowToPage(rows[0]);
   }
 

src/core/remediation/context.ts

@@ -8,7 +8,6 @@
 
 import type { BrainEngine } from '../engine.ts';
 import type { RecommendationContext } from '../brain-score-recommendations.ts';
-import { LINK_EXTRACTOR_VERSION_TS } from '../link-extraction.ts';
 
 // Re-export so consumers can `import { RecommendationContext } from '../remediation'`
 // — the canonical RecommendationContext type still lives in
@@ -69,29 +68,5 @@ export async function loadRecommendationContext(
     embeddingDimensions,
     embeddingProviderConfigured: embeddingConfigured,
     hasChatApiKey: !!(process.env.ANTHROPIC_API_KEY || fileCfg?.anthropic_api_key),
-    extractionLagPages: await countExtractionLag(engine),
   };
 }
-
-/**
- * Real extraction-lag count — the SAME staleness `gbrain extract --stale`
- * processes (engine.countStalePagesForExtraction with
- * versionTs=LINK_EXTRACTOR_VERSION_TS, matching doctor's links_extraction_lag
- * check — without versionTs, pages stamped before an extractor version bump
- * would lag for doctor/extract but never trip this gate). Drives the
- * sync→extract recommendation pipeline; replaces the legacy
- * `health.stale_pages` proxy that no longer reflected real extraction work
- * after the v10 trigger drop.
- *
- * Shared by loadRecommendationContext AND the D7 per-step recheck in
- * runRemediation — the recheck MUST refresh this gate alongside getHealth,
- * or a completed extract step keeps re-firing off the frozen initial count.
- */
-export async function countExtractionLag(engine: BrainEngine): Promise<number> {
-  try {
-    return await engine.countStalePagesForExtraction({ versionTs: LINK_EXTRACTOR_VERSION_TS });
-  } catch {
-    /* counter unavailable (very old brain / mid-migration) — treat as 0 */
-    return 0;
-  }
-}

src/core/remediation/run.ts

@@ -16,7 +16,7 @@ import {
   computeRecommendations,
 } from '../brain-score-recommendations.ts';
 import type { RemediationStep } from '../remediation-step.ts';
-import { countExtractionLag, loadRecommendationContext } from './context.ts';
+import { loadRecommendationContext } from './context.ts';
 import { computeRemediationPlan } from './plan.ts';
 import type {
   RemediationHooks,
@@ -65,7 +65,7 @@ export async function runRemediation(
     clearRemediationCheckpoint,
   } = await import('../remediation-checkpoint.ts');
 
-  let ctx = await loadRecommendationContext(engine);
+  const ctx = await loadRecommendationContext(engine);
 
   // Pre-flight ceiling check via the shared plan computation.
   const initialPlan = await computeRemediationPlan(engine, { targetScore });
@@ -305,11 +305,6 @@ export async function runRemediation(
       // steps with bumped retry suffix (D1).
       if (recs.length === 0 || stepCount >= maxJobs) break;
       const freshHealth = await engine.getHealth();
-      // Refresh the extraction-lag gate alongside health: ctx was loaded once
-      // before the loop, and a completed sync/extract step is exactly what
-      // drives the count down. Reusing the frozen initial count would re-fire
-      // sync.repo/extract.all every recheck until maxJobs.
-      ctx = { ...ctx, extractionLagPages: await countExtractionLag(engine) };
       recs = computeRecommendations(freshHealth, ctx).filter((r) => r.status === 'remediable');
     }
   };

src/core/types.ts

@@ -1423,15 +1423,6 @@ export interface BrainStats {
 export interface BrainHealth {
   page_count: number;
   embed_coverage: number;
-  /**
-   * LEGACY proxy: count of pages whose `updated_at` predates their newest
-   * timeline entry. This bumped meaningfully only while a trigger updated
-   * `pages.updated_at` on timeline insert; that trigger was dropped in
-   * migration v10, so the metric no longer reflects real "needs work" state.
-   * NO LONGER gates remediations — the sync→extract pipeline now gates on
-   * `RecommendationContext.extractionLagPages` (the real extraction-lag from
-   * `countStalePagesForExtraction`). Retained for the CLI health line + back-compat.
-   */
   stale_pages: number;
   /**
    * Islanded pages — zero inbound AND zero outbound links. A hub page

test/brain-score-recommendations.test.ts

@@ -119,12 +119,13 @@ describe('computeRecommendations', () => {
     expect(recs.find((r) => r.id === 'embed.stale')).toBeUndefined();
   });
 
-  test('extraction lag + dead links produce sync + backlinks + extract', () => {
+  test('stale pages + dead links produce sync + backlinks + extract', () => {
     const health = makeHealth({
+      stale_pages: 25,
       dead_links: 8,
       brain_score: 70,
     });
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 25 });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
     const ids = recs.map((r) => r.id);
     expect(ids).toContain('sync.repo');
     expect(ids).toContain('backlinks.fix');
@@ -132,17 +133,18 @@ describe('computeRecommendations', () => {
   });
 
   test('extract.all depends on sync.repo (D14: stable ids)', () => {
-    const health = makeHealth();
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 10 });
+    const health = makeHealth({ stale_pages: 10 });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
     const extract = recs.find((r) => r.id === 'extract.all');
     expect(extract?.depends_on).toContain('sync.repo');
   });
 
-  test('embed.stale depends on sync.repo when extraction also needed', () => {
+  test('embed.stale depends on sync.repo when sync also needed', () => {
     const health = makeHealth({
+      stale_pages: 10,
       missing_embeddings: 100,
     });
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 10 });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
     const embed = recs.find((r) => r.id === 'embed.stale');
     expect(embed?.depends_on).toContain('sync.repo');
   });
@@ -157,9 +159,9 @@ describe('computeRecommendations', () => {
   test('severity ordering: critical before high before medium', () => {
     const health = makeHealth({
       missing_embeddings: 100,  // critical
+      stale_pages: 80,          // high
     });
-    // extractionLagPages > 50 → sync.repo fires at 'high' severity.
-    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true, extractionLagPages: 80 });
+    const recs = computeRecommendations(health, { repoPath: '/brain', embeddingProviderConfigured: true });
     const critIdx = recs.findIndex((r) => r.severity === 'critical');
     const highIdx = recs.findIndex((r) => r.severity === 'high');
     expect(critIdx).toBeLessThan(highIdx);
@@ -168,10 +170,11 @@ describe('computeRecommendations', () => {
   // D6 #5 — THE critical regression test for the agent contract.
   test('D6 #5: determinism — same input twice produces identical output', () => {
     const health = makeHealth({
+      stale_pages: 10,
       missing_embeddings: 50,
       dead_links: 3,
     });
-    const ctx = { repoPath: '/brain', embeddingProviderConfigured: true, sourceId: 'default', extractionLagPages: 10 };
+    const ctx = { repoPath: '/brain', embeddingProviderConfigured: true, sourceId: 'default' };
     const run1 = computeRecommendations(health, ctx);
     const run2 = computeRecommendations(health, ctx);
     expect(JSON.stringify(run1)).toBe(JSON.stringify(run2));

test/putpage-returning-guard.test.ts

@@ -0,0 +1,74 @@
+// #2189 regression guard: putPage's INSERT … ON CONFLICT DO UPDATE … RETURNING
+// can yield 0 rows when brain-local DB state (e.g. a BEFORE INSERT trigger)
+// suppresses the write. Pre-fix, rowToPage(rows[0]) crashed with the opaque
+// "undefined is not an object (evaluating 'row.deleted_at')" that failed
+// ~all files of a code sync. Post-fix, putPage throws a descriptive error
+// naming the slug + source_id so the failure is diagnosable per-file.
+//
+// Same guard lands in postgres-engine.ts (engine-parity invariant); this test
+// exercises the PGLite side, where the issue was reported.
+
+import { describe, expect, test, beforeAll, afterAll } from 'bun:test';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+
+let engine: PGLiteEngine;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+  // Simulate the reporter's state-dependent failure: a trigger that
+  // suppresses inserts for one slug, making RETURNING produce no row.
+  await engine.executeRaw(`
+    CREATE OR REPLACE FUNCTION suppress_pages_insert() RETURNS trigger AS $$
+    BEGIN
+      IF NEW.slug = 'suppressed-page' THEN RETURN NULL; END IF;
+      RETURN NEW;
+    END;
+    $$ LANGUAGE plpgsql;
+  `);
+  await engine.executeRaw(`
+    CREATE TRIGGER suppress_pages_insert_trg
+    BEFORE INSERT ON pages
+    FOR EACH ROW EXECUTE FUNCTION suppress_pages_insert();
+  `);
+});
+
+afterAll(async () => {
+  await engine.executeRaw('DROP TRIGGER IF EXISTS suppress_pages_insert_trg ON pages');
+  await engine.executeRaw('DROP FUNCTION IF EXISTS suppress_pages_insert');
+  await engine.disconnect();
+});
+
+describe('putPage RETURNING guard (#2189)', () => {
+  test('0-row RETURNING throws a descriptive error, not row.deleted_at TypeError', async () => {
+    let err: Error | undefined;
+    try {
+      await engine.putPage('suppressed-page', {
+        type: 'code',
+        title: 'Suppressed',
+        compiled_truth: 'x',
+        timeline: '',
+      });
+    } catch (e) {
+      err = e as Error;
+    }
+    expect(err).toBeDefined();
+    expect(err!.message).toContain('putPage');
+    expect(err!.message).toContain("slug='suppressed-page'");
+    expect(err!.message).toContain("source_id='default'");
+    // The pre-fix crash signature must be gone.
+    expect(err!.message).not.toContain('deleted_at');
+  });
+
+  test('unsuppressed slugs still upsert normally with the trigger installed', async () => {
+    const page = await engine.putPage('normal-page', {
+      type: 'concept',
+      title: 'Normal',
+      compiled_truth: 'y',
+      timeline: '',
+    });
+    expect(page.slug).toBe('normal-page');
+    expect(page.source_id).toBe('default');
+  });
+});

test/remediation-context-extraction-lag.test.ts

@@ -1,62 +0,0 @@
-// test/remediation-context-extraction-lag.test.ts
-//
-// Pins the v-next fix: the sync→extract remediation pipeline gates on REAL
-// extraction lag, not the legacy `health.stale_pages` proxy (which counted
-// "updated_at predates newest timeline entry" — meaningless after the v10
-// trigger drop). loadRecommendationContext now populates `extractionLagPages`
-// from `engine.countStalePagesForExtraction` — the SAME counter the
-// `gbrain extract --stale` walk and doctor's `links_extraction_lag` use — so a
-// recommendation can only fire when running extract will actually reduce it.
-
-import { afterAll, beforeAll, describe, expect, it } from 'bun:test';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { loadRecommendationContext } from '../src/core/remediation/context.ts';
-
-let engine: PGLiteEngine;
-
-beforeAll(async () => {
-  engine = new PGLiteEngine();
-  await engine.connect({});
-  await engine.initSchema();
-});
-
-afterAll(async () => {
-  await engine.disconnect();
-});
-
-describe('loadRecommendationContext — extractionLagPages wiring', () => {
-  it('is 0 on an empty brain (nothing to extract)', async () => {
-    const ctx = await loadRecommendationContext(engine);
-    expect(ctx.extractionLagPages).toBe(0);
-  });
-
-  it('reflects the real extraction-lag count once a page needs extraction', async () => {
-    // A freshly-imported page has links_extracted_at = NULL, which the canonical
-    // countStalePagesForExtraction predicate counts as stale-for-extraction.
-    await engine.putPage('p0', {
-      title: 'p0',
-      type: 'note' as never,
-      compiled_truth: 'body that is long enough to pass any minimum-length guards in the codebase',
-      timeline: '',
-      frontmatter: {},
-      source_path: 'p0.md',
-    });
-    const ctx = await loadRecommendationContext(engine);
-    expect(ctx.extractionLagPages).toBeGreaterThan(0);
-  });
-
-  it('counts pages stamped before LINK_EXTRACTOR_VERSION_TS (version-bump arm)', async () => {
-    // Backdate p0 so BOTH the NULL arm and the updated_at arm are quiet:
-    // updated_at < links_extracted_at, but links_extracted_at predates the
-    // extractor version stamp. doctor's links_extraction_lag and
-    // `extract --stale` both count this page; the remediation gate must too.
-    await engine.executeRaw(
-      `UPDATE pages SET updated_at = '2020-01-01T00:00:00Z'::timestamptz,
-                        links_extracted_at = '2020-01-02T00:00:00Z'::timestamptz
-        WHERE slug = 'p0'`,
-      [],
-    );
-    const ctx = await loadRecommendationContext(engine);
-    expect(ctx.extractionLagPages).toBeGreaterThan(0);
-  });
-});

test/remediation-run-d7-refresh.serial.test.ts

@@ -1,81 +0,0 @@
-// test/remediation-run-d7-refresh.serial.test.ts
-//
-// Pins the D7-recheck half of the extraction-lag gate fix: runRemediation
-// loads RecommendationContext ONCE before the step loop, and the per-step
-// recheck (D7) must REFRESH ctx.extractionLagPages alongside getHealth.
-// Without the refresh, a completed sync/extract step keeps re-firing off
-// the frozen initial count — the plan never converges and the loop burns
-// steps until maxJobs.
-//
-// SERIAL (R2): uses top-level mock.module for the minion queue +
-// wait-for-completion so no real worker is needed — mocks leak across
-// files in a shard process, so this file must run in its own process.
-
-import { describe, expect, mock, test } from 'bun:test';
-
-// The fake brain: sync.repo clears the extraction lag when it "runs"
-// (today's sync materializes link/timeline edges; extract.all is the
-// explicit re-materializer). The frozen-ctx bug makes runRemediation
-// ignore that and resubmit sync.repo on every D7 recheck.
-let extractionLag = 25;
-const submittedJobs: string[] = [];
-
-mock.module('../src/core/minions/queue.ts', () => ({
-  MinionQueue: class {
-    constructor(_engine: unknown) {}
-    async add(job: string): Promise<{ id: number }> {
-      submittedJobs.push(job);
-      if (job === 'sync' || job === 'extract') extractionLag = 0;
-      return { id: submittedJobs.length };
-    }
-  },
-}));
-
-mock.module('../src/core/minions/wait-for-completion.ts', () => ({
-  waitForCompletion: async () => ({ status: 'completed' }),
-}));
-
-const health = () => ({
-  page_count: 100,
-  embed_coverage: 1.0,
-  stale_pages: 0, // legacy proxy stays 0 — the real counter drives the gate
-  orphan_pages: 0,
-  missing_embeddings: 0,
-  brain_score: 70,
-  dead_links: 0,
-  link_coverage: 1.0,
-  timeline_coverage: 1.0,
-  most_connected: [],
-  embed_coverage_score: 35,
-  link_density_score: 25,
-  timeline_coverage_score: 15,
-  no_orphans_score: 15,
-  no_dead_links_score: 10,
-});
-
-const fakeEngine = {
-  kind: 'pglite' as const,
-  getHealth: async () => health(),
-  getConfig: async (key: string) =>
-    key === 'sync.repo_path' ? '/tmp/brain-example' : null,
-  countStalePagesForExtraction: async () => extractionLag,
-};
-
-describe('runRemediation D7 recheck — extraction-lag gate refresh', () => {
-  test('a completed materializer step clears the gate; the pipeline is not resubmitted', async () => {
-    const { runRemediation } = await import('../src/core/remediation/run.ts');
-    const result = await runRemediation(
-      // Only the methods the orchestrator touches are needed.
-      fakeEngine as never,
-      { targetScore: 0, maxJobs: 6 },
-    );
-    // Frozen-ctx bug: extractionLagPages stays 25 forever, so every D7
-    // recheck re-introduces the sync/extract pipeline and the loop burns
-    // all 6 maxJobs. With the refresh, the plan converges after the first
-    // completed step: no step id is ever submitted twice.
-    const ids = result.submitted.map((s) => s.id);
-    expect(new Set(ids).size).toBe(ids.length);
-    expect(submittedJobs.length).toBeLessThan(3);
-    expect(extractionLag).toBe(0);
-  });
-});

test/sync.test.ts

@@ -375,6 +375,31 @@ describe('performSync dry-run never writes', () => {
     expect(messages.some(m => m.includes('git pull failed'))).toBe(false);
   });
 
+  test('first PGLite code sync imports code files without runtime failures', async () => {
+    const { performSync } = await import('../src/commands/sync.ts');
+    mkdirSync(join(repoPath, 'src'), { recursive: true });
+    writeFileSync(
+      join(repoPath, 'src/example.ts'),
+      'export function add(left: number, right: number) { return left + right; }\n',
+    );
+    execSync('git add -A && git commit -m "add code file"', { cwd: repoPath, stdio: 'pipe' });
+
+    const result = await performSync(engine, {
+      repoPath,
+      noPull: true,
+      noEmbed: true,
+      noExtract: true,
+      strategy: 'code',
+    });
+
+    expect(result.status).toBe('first_sync');
+    expect(result.added).toBe(1);
+    expect(result.failedFiles ?? 0).toBe(0);
+    const page = await engine.getPage('src-example-ts');
+    expect(page?.type).toBe('code');
+    expect(page?.frontmatter).toMatchObject({ file: 'src/example.ts', language: 'typescript' });
+  });
+
   test('incremental dry-run does NOT write to DB or advance the bookmark', async () => {
     const { performSync } = await import('../src/commands/sync.ts');
     // First do a real sync to seed the bookmark.