fix(facts): seed phase B backfill row_nums past the DB max (#2044 class)

phaseBFenceFacts appended at fence-max+1 with no DB seeding, so on a
diverged page (stamped DB rows + missing fence at the resolved path —
the same divergence class the writeFactsToFence fix handles) the
post-rename UPDATE hit idx_facts_fence_key, the page failed, and the
already-renamed fence disagreed with the DB while the row_num-NULL
backlog persisted. Seed appended row_nums from MAX(fence max, DB max)
per (source_id, slug), mirroring the fence-write fix. Repro test added.

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

src/cli.ts

@@ -54,7 +54,7 @@ export function bigintToStringReplacer(_key: string, value: unknown): unknown {
 }
 
 // CLI-only commands that bypass the operation layer
-export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
+export const CLI_ONLY = new Set(['init', 'reinit-pglite', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'extract-conversation-facts', 'enrich', 'features', 'autopilot', 'graph-query', 'jobs', 'agent', 'apply-migrations', 'skillpack-check', 'skillpack', 'resolvers', 'integrity', 'repair-jsonb', 'orphans', 'sources', 'mounts', 'dream', 'check-resolvable', 'routing-eval', 'skillify', 'smoke-test', 'providers', 'storage', 'repos', 'code-def', 'code-refs', 'reindex', 'reindex-code', 'reindex-frontmatter', 'code-callers', 'code-callees', 'reconcile-links', 'frontmatter', 'auth', 'friction', 'claw-test', 'book-mirror', 'takes', 'think', 'salience', 'anomalies', 'calibration', 'transcripts', 'models', 'remote', 'recall', 'forget', 'edges-backfill', 'facts', 'cache', 'ze-switch', 'founder', 'brainstorm', 'lsd', 'schema', 'capture', 'onboard', 'conversation-parser', 'status', 'connect', 'skillopt', 'quarantine', 'self-upgrade', 'advisor', 'watch', 'reindex-search-vector']);
 // CLI-only commands whose handlers print their own --help text. These are
 // excluded from the generic short-circuit so detailed per-command and
 // per-subcommand usage stays reachable.
@@ -991,6 +991,8 @@ const THIN_CLIENT_REFUSED_COMMANDS = new Set([
   // hint pointing at the routable MCP tools; per-subcommand splits are
   // a v0.31.x follow-up TODO.
   'takes', 'sources',
+  // #1867: fence-backfill edits local .md fences + stamps the local DB.
+  'facts',
   // v0.32 thin-client routing audit (Codex round 2 findings #2, #4):
   // - `pages` purge-deleted is admin+localOnly (operations.ts:856-864)
   // - `files` list / file_url MCP ops are localOnly (operations.ts:1769-1879)
@@ -1026,6 +1028,7 @@ const THIN_CLIENT_REFUSE_HINTS: Record<string, string> = {
   migrate: "migrate runs on the host's local engine. Run on the host machine.",
   'apply-migrations': 'schema migrations run on the host. SSH and run there.',
   'repair-jsonb': 'repair-jsonb operates on the local DB only.',
+  facts: 'facts fence-backfill edits local entity-page fences. Run on the host machine.',
   integrity: 'integrity scans local files. Run on the host machine.',
   serve: 'serve starts a server. Run on the host, not the thin client.',
   dream: 'dream runs the autopilot cycle on the host. `gbrain remote ping` queues one. (Native `gbrain dream` thin-client routing planned for v0.31.2.)',
@@ -1855,6 +1858,13 @@ async function handleCliOnly(command: string, args: string[]) {
         await runEdgesBackfill(engine, args);
         break;
       }
+      case 'facts': {
+        // #1867 — re-runnable fence-backfill for row_num-NULL legacy fact
+        // rows (idempotent v0_32_2 phase B, exposed as an operator command).
+        const { runFactsCommand } = await import('./commands/facts.ts');
+        await runFactsCommand(engine, args);
+        break;
+      }
       case 'whoknows': {
         // v0.33 (Issue #?): expertise + relationship-proximity routing.
         // MCP op `find_experts` (read-scoped) backs the same code path; CLI
@@ -2335,6 +2345,7 @@ TOOLS
   check-backlinks <check|fix> [dir]  Find/fix missing back-links across brain
   lint <dir|file> [--fix]            Catch LLM artifacts, placeholder dates, bad frontmatter
   orphans [--json] [--count]         Find pages with no inbound wikilinks
+  facts fence-backfill [--dry-run]   Fence legacy fact rows (row_num NULL) onto entity pages
   salience [--days N] [--kind P]     v0.29: pages ranked by emotional + activity salience
   anomalies [--since D] [--sigma N]  v0.29: cohort-based statistical anomalies (tag, type)
   transcripts recent [--days N]      v0.29: recent raw .txt transcripts (local-only)

src/commands/extract.ts

@@ -1651,7 +1651,7 @@ async function extractTimelineFromDB(
  * make re-extraction idempotent). EVERY processed page is stamped, including
  * zero-link pages — they WERE processed.
  */
-export async function extractStaleFromDB(
+async function extractStaleFromDB(
   engine: BrainEngine,
   opts: {
     dryRun: boolean;

src/commands/facts.ts

@@ -0,0 +1,48 @@
+/**
+ * gbrain facts — fact-store maintenance surface (#1867).
+ *
+ * `fence-backfill` re-runs the v0_32_2 fence-backfill phase on demand.
+ * Remote `extract_facts` deposits that predate the fence-write backstop
+ * (and any legacy DB-only insert) leave `row_num IS NULL` rows that the
+ * cycle extract_facts guard refuses to reconcile past — previously the
+ * only remedy was the one-shot v0_32_2 migration, which the ledger marks
+ * complete and never re-runs. The phase is idempotent (only touches
+ * `row_num IS NULL` rows), so exposing it as a command is safe to re-run
+ * any time the backlog reappears.
+ */
+import type { BrainEngine } from '../core/engine.ts';
+import { setCliExitVerdict } from '../core/cli-force-exit.ts';
+import { phaseBFenceFacts } from './migrations/v0_32_2.ts';
+
+function printHelp(): void {
+  process.stderr.write(
+    `Usage: gbrain facts fence-backfill [--dry-run]\n\n` +
+      `Fence-backfill: appends every legacy fact row (row_num IS NULL) to its\n` +
+      `entity page's \`## Facts\` fence and stamps row_num + source_markdown_slug\n` +
+      `back onto the DB row. Idempotent — re-runs only pick up rows still\n` +
+      `missing a fence assignment. Clears the backlog that makes the cycle's\n` +
+      `extract_facts phase skip fence→DB reconciliation.\n\n` +
+      `  --dry-run   report what would be fenced; no FS or DB writes\n`,
+  );
+}
+
+export async function runFactsCommand(engine: BrainEngine, args: string[]): Promise<void> {
+  const sub = args[0];
+  if (!sub || sub === '--help' || sub === '-h') {
+    printHelp();
+    return;
+  }
+  if (sub !== 'fence-backfill') {
+    process.stderr.write(`Unknown facts subcommand: ${sub}\n`);
+    printHelp();
+    setCliExitVerdict(1);
+    return;
+  }
+
+  const dryRun = args.includes('--dry-run');
+  const result = await phaseBFenceFacts(engine, { dryRun });
+  process.stderr.write(
+    `fence-backfill: ${result.status}${result.detail ? ` — ${result.detail}` : ''}\n`,
+  );
+  if (result.status === 'failed') setCliExitVerdict(1);
+}

src/commands/jobs.ts

@@ -1479,31 +1479,7 @@ export async function registerBuiltinHandlers(
       embedSkipReason = 'auto_embed_disabled';
     }
 
-    // #2849: large-sync extract deferral follow-up. performSync skips inline
-    // link/timeline extraction when totalChanges > 100, leaving
-    // links_extracted_at unstamped. A standalone sync job (webhook push,
-    // sync trigger) has no autopilot extract phase behind it, so the pages
-    // would stay extraction-stale until a manual `gbrain extract --stale`.
-    // Queue a source-scoped stale sweep instead. Best-effort + idempotent:
-    // a duplicate sweep finds 0 stale pages and no-ops.
-    let extractJobId: number | null = null;
-    if (result.extractDeferred) {
-      try {
-        const { MinionQueue } = await import('../core/minions/queue.ts');
-        const queue = new MinionQueue(engine);
-        const followUp = await queue.add(
-          'extract',
-          { stale: true, ...(sourceId ? { sourceId } : {}) },
-          {
-            idempotency_key: `sync-extract-stale:${sourceId ?? 'default'}:${Math.floor(Date.now() / 30_000)}`,
-            maxWaiting: 1,
-          },
-        );
-        extractJobId = followUp.id;
-      } catch { /* best-effort: extract --stale sweeps it later */ }
-    }
-
-    return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason, extract_stale_job_id: extractJobId };
+    return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason };
   });
 
   registerBuiltinJob(worker, engine, 'embed', async (job) => {
@@ -1676,20 +1652,6 @@ export async function registerBuiltinHandlers(
   });
 
   worker.register('extract', async (job) => {
-    // #2849: stale-sweep mode — the sync handler's large-sync deferral
-    // follow-up. DB-source (reads page content from the DB, so it runs on
-    // checkout-less brains), source-scopable, idempotent. Same core as
-    // `gbrain extract --stale`.
-    if (job.data.stale === true) {
-      const { extractStaleFromDB } = await import('./extract.ts');
-      return await extractStaleFromDB(engine, {
-        dryRun: !!job.data.dryRun,
-        jsonMode: false,
-        includeFrontmatter: false,
-        sourceIdFilter: typeof job.data.sourceId === 'string' ? job.data.sourceId : undefined,
-        catchUp: false,
-      });
-    }
     const { runExtractCore } = await import('./extract.ts');
     const mode = (typeof job.data.mode === 'string' && ['links', 'timeline', 'all'].includes(job.data.mode))
       ? (job.data.mode as 'links' | 'timeline' | 'all')

src/commands/migrations/v0_32_2.ts

@@ -39,6 +39,7 @@ import type { BrainEngine } from '../../core/engine.ts';
 import { loadConfig, toEngineConfig } from '../../core/config.ts';
 import { createEngine } from '../../core/engine-factory.ts';
 import { upsertFactRow, parseFactsFence } from '../../core/facts-fence.ts';
+import { resolvePageFilePath } from '../../core/markdown.ts';
 
 let testEngineOverride: BrainEngine | null = null;
 export function __setTestEngineOverride(engine: BrainEngine | null): void {
@@ -148,9 +149,16 @@ function isLocalPathDirty(localPath: string): boolean {
   }
 }
 
-async function phaseBFenceFacts(
+/**
+ * Exported (not just via `__testing`) because `gbrain facts fence-backfill`
+ * (#1867) re-runs this phase on demand: remote `extract_facts` deposits that
+ * predate the fence-write backstop leave row_num-NULL rows the cycle guard
+ * refuses to reconcile past. The phase is idempotent (only touches
+ * `row_num IS NULL` rows), so re-running is always safe.
+ */
+export async function phaseBFenceFacts(
   engine: BrainEngine | null,
-  opts: OrchestratorOpts,
+  opts: Pick<OrchestratorOpts, 'dryRun'>,
 ): Promise<OrchestratorPhaseResult> {
   if (opts.dryRun) {
     // Dry-run: report what WOULD happen without touching FS or DB.
@@ -238,7 +246,11 @@ async function phaseBFenceFacts(
     for (const [key, group] of groups) {
       const [sourceId, entitySlug] = key.split('\0');
       const localPath = localPathById.get(sourceId)!;
-      const filePath = join(localPath, `${entitySlug}.md`);
+      // resolvePageFilePath, NOT a bare join — non-default sources fence
+      // into `<local_path>/.sources/<id>/<slug>.md`, the same path the
+      // fence-write backstop and put_page write-through compute. A bare
+      // join here diverges fence and DB for non-default sources (#2044).
+      const filePath = resolvePageFilePath(localPath, entitySlug, sourceId);
       const tmpPath = `${filePath}.tmp`;
 
       try {
@@ -269,6 +281,21 @@ async function phaseBFenceFacts(
         const existingFence = parseFactsFence(body);
         const existingKeySet = new Set(existingFence.facts.map(f => `${f.claim}\0${f.source ?? ''}`));
 
+        // Seed appended row_nums from MAX(fence max, DB max) — same #2044
+        // divergence guard as writeFactsToFence. When the fence at the
+        // resolved path is missing/behind but the DB already holds stamped
+        // rows for this slug (legacy wrong-path fence writes), fence-max+1
+        // collides with idx_facts_fence_key on the post-rename UPDATE,
+        // failing the page and leaving fence and DB disagreeing.
+        const dbMaxRows = await engine.executeRaw<{ max: number | string | null }>(
+          `SELECT MAX(row_num) AS max FROM facts
+            WHERE source_id = $1 AND source_markdown_slug = $2`,
+          [sourceId, entitySlug],
+        );
+        const dbMaxRowNum = Number(dbMaxRows[0]?.max ?? 0) || 0;
+        const fenceMaxRowNum = existingFence.facts.reduce((m, f) => Math.max(m, f.rowNum), 0);
+        let nextRowNum = Math.max(fenceMaxRowNum, dbMaxRowNum) + 1;
+
         const assignments: Array<{ id: string; row_num: number }> = [];
         for (const row of group) {
           const key = `${row.fact}\0${row.source ?? ''}`;
@@ -291,6 +318,7 @@ async function phaseBFenceFacts(
                 .toISOString().slice(0, 10)
             : undefined;
           const { body: updated, rowNum } = upsertFactRow(body, {
+            rowNum:     nextRowNum++,
             claim:      row.fact,
             kind:       row.kind,
             confidence: row.confidence,
@@ -381,7 +409,7 @@ async function phaseCVerify(
     for (const g of groups) {
       const localPath = localPathById.get(g.source_id);
       if (!localPath) continue;
-      const filePath = join(localPath, `${g.source_markdown_slug}.md`);
+      const filePath = resolvePageFilePath(localPath, g.source_markdown_slug, g.source_id);
       if (!existsSync(filePath)) {
         mismatches.push(`${g.source_markdown_slug} (file missing)`);
         continue;

src/commands/serve-http.ts

@@ -2146,13 +2146,8 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
   //     Other event types (ping, pull_request, etc.) return 202 'ignored'
   //     so GitHub doesn't retry.
   // D15.5: HMAC compare uses the shared safeHexEqual helper.
-  // D18: submits 'sync' job with extraction + auto_embed_backfill enabled and
-  //     priority -10 (above autopilot's 0). noExtract:false opts normal
-  //     incremental pushes into sync's inline link/timeline extraction (#2849
-  //     — the standalone sync handler defaults noExtract to TRUE, which left
-  //     webhook-imported pages permanently stale). Large (>100 file) pushes
-  //     defer inline extract; the sync handler queues an extract --stale
-  //     follow-up job for that branch.
+  // D18: submits 'sync' job with auto_embed_backfill=true and priority -10
+  //     (above autopilot's 0).
   // ---------------------------------------------------------------------------
   const githubWebhookLimiter = rateLimit({
     windowMs: 60_000,
@@ -2272,7 +2267,6 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
           'sync',
           {
             sourceId: source.id,
-            noExtract: false,
             auto_embed_backfill: true,
             embed_reason: 'webhook',
           },

src/commands/sync.ts

@@ -222,14 +222,6 @@ export interface SyncResult {
    * everything," the exact misdiagnosis in the #1794 recurrence report.
    */
   bankedFiles?: number;
-  /**
-   * #2849: true when extraction was REQUESTED (noExtract false) but this sync
-   * skipped inline link/timeline extraction because totalChanges > 100 (the
-   * #1794 large-sync deferral). links_extracted_at stays unstamped for the
-   * imported pages. The standalone `sync` job handler queues a source-scoped
-   * `extract --stale` follow-up when set; CLI runs print the manual hint.
-   */
-  extractDeferred?: boolean;
 }
 
 /**
@@ -1387,10 +1379,6 @@ See also:
     {
       sourceId: sourceIdArg,
       repoPath: source.local_path,
-      // #2849: opt in to inline extraction — the standalone sync handler
-      // defaults noExtract to TRUE (dedupe for doctor's [sync, extract]
-      // remediation plan), which would leave triggered syncs extraction-stale.
-      noExtract: false,
       auto_embed_backfill: true,
       embed_reason: 'sync_trigger',
     },
@@ -3299,16 +3287,11 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
   // the stale sweep scans the whole source, so banked-across-runs pages are
   // covered regardless.
   const extractOpts = opts.sourceId ? { sourceId: opts.sourceId } : undefined;
-  let extractDeferred = false;
   if (!opts.noExtract && totalChanges > 100 && pagesAffected.length > 0) {
-    // #2849: surface the deferral to callers. A standalone sync job (webhook
-    // push, sync trigger) has no autopilot extract phase behind it, so the
-    // job handler queues an `extract --stale` follow-up off this flag.
-    extractDeferred = true;
     slog(
       `  Large sync: deferring link/timeline extraction. ` +
       `Run 'gbrain extract --stale${opts.sourceId ? ` --source-id ${opts.sourceId}` : ''}' ` +
-      `(sync jobs queue this follow-up automatically).`,
+      `(or let the autopilot cycle's extract phase sweep it).`,
     );
   }
   if (!opts.noExtract && totalChanges <= 100 && pagesAffected.length > 0) {
@@ -3417,7 +3400,6 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
     chunksCreated,
     embedded,
     pagesAffected,
-    extractDeferred,
   };
 }
 

src/core/cycle/extract-facts.ts

@@ -176,9 +176,11 @@ export async function runExtractFacts(
   if (legacyCount > 0) {
     result.guardTriggered = true;
     result.warnings.push(
-      `extract_facts: ${legacyCount} legacy v0.31 fact rows pending fence backfill. ` +
-      `Run \`gbrain apply-migrations --yes\` to complete v0_32_2 before this phase ` +
-      `can safely reconcile fence → DB.`,
+      `extract_facts: ${legacyCount} legacy fact rows pending fence backfill ` +
+      `(row_num IS NULL — v0.31 rows or remote extract_facts deposits that ` +
+      `predate the fence backstop). Run \`gbrain facts fence-backfill\` ` +
+      `(idempotent, re-runnable) before this phase can safely reconcile ` +
+      `fence → DB.`,
     );
     return result;
   }

src/core/engine.ts

@@ -1739,13 +1739,14 @@ export interface BrainEngine {
    * single-row supersede flow because fence reconciliation is the canonical
    * source-of-truth direction, not the consolidator path.
    *
-   * Insertion is atomic per call: all rows commit in a single transaction
-   * or none commit (the transaction rolls back on any constraint
-   * violation, e.g. the v51 partial UNIQUE index on
-   * `(source_id, source_markdown_slug, row_num)`).
+   * Insertion runs in a single transaction. A collision on the v51
+   * partial UNIQUE index `(source_id, source_markdown_slug, row_num)`
+   * skips ONLY that row (ON CONFLICT DO NOTHING, #2044) — the rest of
+   * the batch still commits, so a redundant deposit against an
+   * already-indexed fence row is idempotent instead of a hard failure.
    *
-   * Returns the inserted ids in input-order so callers can correlate
-   * fence-row → DB-id without a separate lookup.
+   * Returns the inserted ids in input-order (colliding rows omitted) so
+   * callers can correlate fence-row → DB-id without a separate lookup.
    */
   insertFacts(
     rows: Array<NewFact & { row_num: number; source_markdown_slug: string }>,

src/core/facts/fence-write.ts

@@ -218,11 +218,27 @@ export async function writeFactsToFence(
       }
 
       // 2. Upsert each fact onto the fence in input order. row_num
-      //    monotonically increases (max-existing + 1 per call, append-only).
+      //    monotonically increases, append-only, seeded from the MAX of
+      //    the fence and the DB index (#2044): when fence and DB have
+      //    diverged (e.g. legacy writes that stamped DB rows against a
+      //    fence at a path this code no longer reads), fence-max+1 can
+      //    collide with an existing DB row_num, tripping
+      //    idx_facts_fence_key and rolling back the whole batch.
+      const dbMaxRows = await engine.executeRaw<{ max: number | string | null }>(
+        `SELECT MAX(row_num) AS max FROM facts
+          WHERE source_id = $1 AND source_markdown_slug = $2`,
+        [target.sourceId, target.slug],
+      );
+      const dbMaxRowNum = Number(dbMaxRows[0]?.max ?? 0) || 0;
+      const fenceMaxRowNum = parseFactsFence(body).facts
+        .reduce((m, f) => Math.max(m, f.rowNum), 0);
+      let nextRowNum = Math.max(fenceMaxRowNum, dbMaxRowNum) + 1;
+
       const assignedRowNums: number[] = [];
       for (const f of facts) {
         const validFromStr = (f.validFrom ?? new Date()).toISOString().slice(0, 10);
         const { body: updated, rowNum } = upsertFactRow(body, {
+          rowNum:      nextRowNum++,
           claim:       f.fact,
           kind:        (f.kind ?? 'fact') as 'fact' | 'event' | 'preference' | 'commitment' | 'belief',
           confidence:  f.confidence ?? 1.0,

src/core/pglite-engine.ts

@@ -4102,11 +4102,13 @@ export class PGLiteEngine implements BrainEngine {
   ): Promise<{ inserted: number; ids: number[] }> {
     if (rows.length === 0) return { inserted: 0, ids: [] };
 
-    // Single transaction so the v51 partial UNIQUE index can roll back the
-    // whole batch on constraint violation. Per-row INSERTs (not multi-row
-    // VALUES) keep the embedding-vs-no-embedding branching readable; batch
-    // sizes are small (5-30 rows per page in practice) so the loop overhead
-    // is negligible vs the embedding compute cost.
+    // Single transaction; per-row INSERTs (not multi-row VALUES) keep the
+    // embedding-vs-no-embedding branching readable; batch sizes are small
+    // (5-30 rows per page in practice) so the loop overhead is negligible
+    // vs the embedding compute cost. #2044: ON CONFLICT DO NOTHING on the
+    // v51 partial UNIQUE index makes a residual fence/DB row_num collision
+    // skip that row instead of rolling back the whole batch (parity with
+    // postgres-engine.ts).
     const ids = await this.db.transaction(async (tx) => {
       const out: number[] = [];
       for (const input of rows) {
@@ -4149,7 +4151,11 @@ export class PGLiteEngine implements BrainEngine {
                  $14, $15,
                  $16, $17, $18, $19,
                  $20
-               ) RETURNING id`
+               )
+               ON CONFLICT (source_id, source_markdown_slug, row_num)
+                 WHERE row_num IS NOT NULL
+                 DO NOTHING
+               RETURNING id`
             : `INSERT INTO facts (
                  source_id, entity_slug, fact, kind, visibility, notability, context,
                  valid_from, valid_until, source, source_session, confidence,
@@ -4163,12 +4169,16 @@ export class PGLiteEngine implements BrainEngine {
                  $15, $16,
                  $17, $18, $19, $20,
                  $21
-               ) RETURNING id`,
+               )
+               ON CONFLICT (source_id, source_markdown_slug, row_num)
+                 WHERE row_num IS NOT NULL
+                 DO NOTHING
+               RETURNING id`,
           embedStr === null
             ? [ctx.source_id, entitySlug, input.fact, kind, visibility, notability, context, validFrom, validUntil, input.source, sourceSession, confidence, embeddedAt, input.row_num, input.source_markdown_slug, claimMetric, claimValue, claimUnit, claimPeriod, eventType]
             : [ctx.source_id, entitySlug, input.fact, kind, visibility, notability, context, validFrom, validUntil, input.source, sourceSession, confidence, embedStr, embeddedAt, input.row_num, input.source_markdown_slug, claimMetric, claimValue, claimUnit, claimPeriod, eventType],
         );
-        out.push(ins.rows[0].id);
+        if (ins.rows[0]) out.push(ins.rows[0].id);
       }
       return out;
     });

src/core/postgres-engine.ts

@@ -4302,10 +4302,12 @@ export class PostgresEngine implements BrainEngine {
     // ONCE per process so the cast matches the actual column type
     // (halfvec vs vector). The probe is cached after first call.
     const castSuffix = await this.resolveFactsEmbeddingCast();
-    // Single transaction so the v51 partial UNIQUE index can roll back
-    // the whole batch on constraint violation. Per-row INSERTs (not
-    // multi-row VALUES) keep the embedding-vs-no-embedding branching
-    // readable; batch sizes are small (5-30 rows per page in practice).
+    // Single transaction; per-row INSERTs (not multi-row VALUES) keep the
+    // embedding-vs-no-embedding branching readable; batch sizes are small
+    // (5-30 rows per page in practice). #2044: ON CONFLICT DO NOTHING on
+    // the v51 partial UNIQUE index makes a residual fence/DB row_num
+    // collision skip that row instead of rolling back the whole batch —
+    // the fence stays system-of-record and reconciliation catches up.
     // No supersede flow in this path — fence reconciliation is the
     // canonical source-of-truth direction, not the consolidator path.
     const ids = await sql.begin(async (tx) => {
@@ -4346,9 +4348,13 @@ export class PostgresEngine implements BrainEngine {
             ${input.row_num}, ${input.source_markdown_slug},
             ${claimMetric}, ${claimValue}, ${claimUnit}, ${claimPeriod},
             ${eventType}
-          ) RETURNING id
+          )
+          ON CONFLICT (source_id, source_markdown_slug, row_num)
+            WHERE row_num IS NOT NULL
+            DO NOTHING
+          RETURNING id
         `;
-        out.push(Number(ins[0].id));
+        if (ins[0]) out.push(Number(ins[0].id));
       }
       return out;
     });

test/extract-facts-phase.test.ts

@@ -304,7 +304,9 @@ describe('runExtractFacts — empty-fence guard (Codex R2-#7)', () => {
     expect(r.legacyRowsPending).toBe(1);
     expect(r.factsInserted).toBe(0);
     expect(r.factsDeleted).toBe(0);
-    expect(r.warnings.some(w => w.includes('apply-migrations'))).toBe(true);
+    // #1867: the remedy hint points at the re-runnable backfill command,
+    // not the one-shot v0_32_2 migration (which the ledger never re-runs).
+    expect(r.warnings.some(w => w.includes('gbrain facts fence-backfill'))).toBe(true);
 
     // Legacy row was NOT touched.
     // eslint-disable-next-line @typescript-eslint/no-explicit-any

test/facts-fence-backfill-command.test.ts

@@ -0,0 +1,133 @@
+/**
+ * #1867 — `gbrain facts fence-backfill` command tests.
+ *
+ * The command re-runs the (idempotent) v0_32_2 phase B on demand so
+ * row_num-NULL backlogs — remote extract_facts deposits that predate
+ * the fence-write backstop — can be cleared without re-running the
+ * one-shot migration. Real PGLite + real tempdir filesystem.
+ */
+
+import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
+import { mkdtempSync, rmSync, existsSync, readFileSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { runFactsCommand } from '../src/commands/facts.ts';
+import { phaseBFenceFacts } from '../src/commands/migrations/v0_32_2.ts';
+
+let engine: PGLiteEngine;
+let brainDir: string;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+});
+
+afterAll(async () => {
+  await engine.disconnect();
+  try {
+    if (brainDir) rmSync(brainDir, { recursive: true, force: true });
+  } catch { /* best-effort */ }
+});
+
+beforeEach(async () => {
+  brainDir = mkdtempSync(join(tmpdir(), 'facts-backfill-cmd-test-'));
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  await (engine as any).db.query('DELETE FROM facts');
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  await (engine as any).db.query(
+    `UPDATE sources SET local_path = $1 WHERE id = 'default'`,
+    [brainDir],
+  );
+});
+
+async function seedLegacyFact(fact: string): Promise<void> {
+  // The row_num-NULL shape a remote extract_facts deposit leaves behind
+  // when it lands via the legacy DB-only path.
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  await (engine as any).db.query(
+    `INSERT INTO facts (source_id, entity_slug, fact, kind, visibility, notability,
+                        valid_from, source, confidence)
+     VALUES ('default', 'people/alice', $1, 'fact', 'private', 'medium',
+             now(), 'mcp:extract_facts', 1.0)`,
+    [fact],
+  );
+}
+
+describe('gbrain facts fence-backfill', () => {
+  test('fences row_num-NULL rows and stamps the DB', async () => {
+    await seedLegacyFact('Deposited remotely');
+
+    await runFactsCommand(engine, ['fence-backfill']);
+
+    // The fence exists on disk with the claim.
+    const filePath = join(brainDir, 'people/alice.md');
+    expect(existsSync(filePath)).toBe(true);
+    expect(readFileSync(filePath, 'utf-8')).toContain('Deposited remotely');
+
+    // The backlog is cleared: no row_num-NULL rows remain.
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const rows = await (engine as any).db.query(
+      'SELECT row_num, source_markdown_slug FROM facts',
+    );
+    expect(rows.rows).toHaveLength(1);
+    expect(rows.rows[0].row_num).toBe(1);
+    expect(rows.rows[0].source_markdown_slug).toBe('people/alice');
+  });
+
+  test('re-run is a no-op (idempotent)', async () => {
+    await seedLegacyFact('Deposited remotely');
+    await runFactsCommand(engine, ['fence-backfill']);
+    await runFactsCommand(engine, ['fence-backfill']);
+
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const rows = await (engine as any).db.query('SELECT id FROM facts');
+    expect(rows.rows).toHaveLength(1);
+    const body = readFileSync(join(brainDir, 'people/alice.md'), 'utf-8');
+    expect(body.match(/Deposited remotely/g)).toHaveLength(1);
+  });
+
+  test('--dry-run reports without writing', async () => {
+    await seedLegacyFact('Deposited remotely');
+    await runFactsCommand(engine, ['fence-backfill', '--dry-run']);
+
+    expect(existsSync(join(brainDir, 'people/alice.md'))).toBe(false);
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const rows = await (engine as any).db.query(
+      'SELECT row_num FROM facts',
+    );
+    expect(rows.rows[0].row_num).toBeNull();
+  });
+
+  test('diverged page: appends past the DB row_num max instead of colliding (#2044 class)', async () => {
+    // The #2044 divergence shape the backfill must survive: the DB already
+    // holds stamped rows 1..3 for the slug (legacy wrong-path fence write),
+    // but the fence at the resolved path is missing. Fence-max+1 (= 1) would
+    // collide with the stamped rows on the post-rename UPDATE, failing the
+    // page and leaving the renamed fence disagreeing with the DB.
+    for (let n = 1; n <= 3; n++) {
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      await (engine as any).db.query(
+        `INSERT INTO facts (source_id, entity_slug, fact, kind, visibility, notability,
+                            valid_from, source, confidence, row_num, source_markdown_slug)
+         VALUES ('default', 'people/alice', $1, 'fact', 'private', 'medium',
+                 now(), 'mcp:extract_facts', 1.0, $2, 'people/alice')`,
+        [`stamped ${n}`, n],
+      );
+    }
+    await seedLegacyFact('Deposited remotely');
+
+    const result = await phaseBFenceFacts(engine, { dryRun: false });
+    expect(result.status).toBe('complete');
+
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const rows = await (engine as any).db.query(
+      `SELECT row_num FROM facts WHERE fact = 'Deposited remotely'`,
+    );
+    expect(rows.rows[0].row_num).toBe(4);
+    const body = readFileSync(join(brainDir, 'people/alice.md'), 'utf-8');
+    expect(body).toContain('| 4 | Deposited remotely |');
+  });
+});

test/fence-write.test.ts

@@ -292,6 +292,49 @@ describe('lookupSourceLocalPath', () => {
   });
 });
 
+describe('writeFactsToFence — fence/DB divergence (#2044)', () => {
+  test('seeds row_num past the DB max when the fence lags the DB', async () => {
+    // Simulate the divergence class from #2044: DB rows were stamped with
+    // row_nums against a fence written at a path this code no longer reads
+    // (e.g. the pre-"Local patch 2026-06-11" wrong-path writes). The page
+    // on disk has NO fence, but the DB already holds row_num 1..3 for the
+    // slug. Pre-fix, the next deposit re-assigned row_num=1 from fence
+    // text alone and the whole insertFacts batch failed on
+    // idx_facts_fence_key.
+    for (let n = 1; n <= 3; n++) {
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      await (engine as any).db.query(
+        `INSERT INTO facts (source_id, entity_slug, fact, kind, visibility, notability,
+                            valid_from, source, confidence, row_num, source_markdown_slug)
+         VALUES ('default', 'people/dana', $1, 'fact', 'private', 'medium',
+                 now(), 'mcp:extract_facts', 1.0, $2, 'people/dana')`,
+        [`old claim ${n}`, n],
+      );
+    }
+
+    const result = await writeFactsToFence(
+      engine,
+      { sourceId: 'default', localPath: brainDir, slug: 'people/dana' },
+      [baseInput({ fact: 'second deposit' })],
+    );
+
+    expect(result.fenceWriteFailed).toBeUndefined();
+    expect(result.inserted).toBe(1);
+
+    // The new row landed PAST the DB max, not at fence-max+1 (= 1).
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const rows = await (engine as any).db.query(
+      'SELECT row_num FROM facts WHERE id = $1',
+      [result.ids[0]],
+    );
+    expect(rows.rows[0].row_num).toBe(4);
+
+    // And the on-disk fence carries the same row_num — fence and DB agree.
+    const body = readFileSync(join(brainDir, 'people/dana.md'), 'utf-8');
+    expect(body).toContain('| 4 | second deposit |');
+  });
+});
+
 // Cleanup any leftover tempdirs after the whole suite.
 afterAll(() => {
   // No-op: each test cleaned up via the beforeEach; this is a safety net.

test/insert-facts-batch.test.ts

@@ -5,7 +5,7 @@
  *   - Batch insert N rows persists row_num + source_markdown_slug
  *   - Empty batch is a no-op
  *   - Returns ids in input-order
- *   - v51 partial UNIQUE index rolls back the whole batch on a collision
+ *   - v51 partial UNIQUE collision skips only the colliding row (#2044)
  *   - deleteFactsForPage scopes by (source_id, source_markdown_slug);
  *     never touches other pages or pre-v51 NULL-source_markdown_slug rows
  *   - deleteFactsForPage on an empty page returns deleted:0 (idempotent)
@@ -135,30 +135,29 @@ describe('engine.insertFacts — batch insert', () => {
     });
   });
 
-  test('v51 partial UNIQUE index rolls back the whole batch on collision', async () => {
+  test('v51 partial UNIQUE collision skips ONLY the colliding row (#2044)', async () => {
     // Seed row #1 first.
     await engine.insertFacts([fixtureFact(1, { fact: 'seeded' })], { source_id: 'default' });
 
-    // Now try to batch-insert rows that include a colliding row_num=1.
-    let threw = false;
-    try {
-      await engine.insertFacts(
-        [
-          fixtureFact(2, { fact: 'second' }),
-          fixtureFact(1, { fact: 'collides' }),  // row_num=1 on same (source_id, source_markdown_slug)
-          fixtureFact(3, { fact: 'third' }),
-        ],
-        { source_id: 'default' },
-      );
-    } catch {
-      threw = true;
-    }
-    expect(threw).toBe(true);
+    // Batch-insert rows that include a colliding row_num=1. Pre-#2044 this
+    // threw and rolled back the whole batch, making a second remote
+    // extract_facts deposit to an already-fenced page a hard failure. Now
+    // ON CONFLICT DO NOTHING skips the colliding row and keeps the rest.
+    const result = await engine.insertFacts(
+      [
+        fixtureFact(2, { fact: 'second' }),
+        fixtureFact(1, { fact: 'collides' }),  // row_num=1 on same (source_id, source_markdown_slug)
+        fixtureFact(3, { fact: 'third' }),
+      ],
+      { source_id: 'default' },
+    );
+    expect(result.inserted).toBe(2);
+    expect(result.ids).toHaveLength(2);
 
-    // Verify the transaction rolled back — only the seeded row should remain.
+    // The seeded row survives untouched; the colliding claim is skipped.
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const rows = await (engine as any).db.query('SELECT fact FROM facts ORDER BY id');
-    expect(rows.rows.map((r: { fact: string }) => r.fact)).toEqual(['seeded']);
+    expect(rows.rows.map((r: { fact: string }) => r.fact)).toEqual(['seeded', 'second', 'third']);
   });
 
   test('different source_markdown_slug values DO NOT collide on the same row_num', async () => {

test/sources-webhook.test.ts

@@ -16,7 +16,6 @@
  */
 import { describe, test, expect } from 'bun:test';
 import { createHmac } from 'node:crypto';
-import { readFileSync } from 'node:fs';
 import { safeHexEqual } from '../src/core/timing-safe.ts';
 
 const GITHUB_SECRET = 'super-secret-webhook-key';
@@ -124,25 +123,3 @@ describe('Branch ref construction (D5)', () => {
     expect(pushedRef === `refs/heads/${trackedBranch}`).toBe(false);
   });
 });
-
-describe('Webhook sync job extraction contract (#2849)', () => {
-  test('opts into extraction before the pushed commit is consumed', () => {
-    const serveSource = readFileSync(
-      new URL('../src/commands/serve-http.ts', import.meta.url),
-      'utf8',
-    );
-    const routeStart = serveSource.indexOf("'/webhooks/github'");
-    const queueStart = serveSource.indexOf('const job = await queue.add(', routeStart);
-    const responseStart = serveSource.indexOf('res.status(202)', queueStart);
-    expect(routeStart).toBeGreaterThanOrEqual(0);
-    expect(queueStart).toBeGreaterThan(routeStart);
-    expect(responseStart).toBeGreaterThan(queueStart);
-
-    const routeSource = serveSource.slice(queueStart, responseStart);
-    const payload = routeSource.match(
-      /queue\.add\(\s*'sync',\s*\{([\s\S]*?)\}\s*,\s*\{/,
-    );
-    expect(payload).not.toBeNull();
-    expect(payload?.[1]).toMatch(/\bnoExtract:\s*false\b/);
-  });
-});

test/sync-large-deferral-extract.serial.test.ts

@@ -1,130 +0,0 @@
-/**
- * #2849 — large-sync extract deferral queues an `extract --stale` follow-up.
- *
- * performSync's incremental path skips inline link/timeline extraction when
- * totalChanges > 100 (the #1794 large-sync deferral), leaving
- * links_extracted_at unstamped. Pre-fix, a standalone sync job (webhook push,
- * `gbrain sync trigger`) had NOTHING behind it to sweep those pages — the
- * autopilot cycle's extract phase only walks that cycle's changedSlugs — so a
- * large webhook push left extraction permanently stale until a manual
- * `gbrain extract --stale`.
- *
- * Pins:
- *   (a) performSync surfaces `extractDeferred: true` on the >100 branch and
- *       leaves the pages unstamped/unlinked.
- *   (b) the `sync` job handler queues an `extract` job with
- *       { stale: true, sourceId? } when extractDeferred is set.
- *   (c) the `extract` handler's stale mode actually sweeps: links created +
- *       watermark stamped (end-to-end recovery, no manual step).
- *
- * Marked .serial.test.ts — spawns git subprocesses + shares one PGLite engine.
- */
-
-import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
-import { mkdtempSync, writeFileSync, rmSync, mkdirSync } from 'fs';
-import { execSync } from 'child_process';
-import { tmpdir } from 'os';
-import { join } from 'path';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { MinionWorker } from '../src/core/minions/worker.ts';
-import { MinionQueue } from '../src/core/minions/queue.ts';
-import { registerBuiltinHandlers } from '../src/commands/jobs.ts';
-
-let engine: PGLiteEngine;
-let worker: MinionWorker;
-let repoPath: string;
-
-function git(cmd: string): void { execSync(cmd, { cwd: repoPath, stdio: 'pipe' }); }
-
-describe('#2849 — large sync defers extract and queues a stale sweep', () => {
-  beforeAll(async () => {
-    engine = new PGLiteEngine();
-    await engine.connect({});
-    await engine.initSchema();
-    worker = new MinionWorker(engine, { queue: 'test' });
-    await registerBuiltinHandlers(worker, engine, { quiet: true });
-
-    repoPath = mkdtempSync(join(tmpdir(), 'gbrain-large-defer-'));
-    git('git init');
-    git('git config user.email "t@t.com"');
-    git('git config user.name "T"');
-    mkdirSync(join(repoPath, 'people'), { recursive: true });
-    mkdirSync(join(repoPath, 'notes'), { recursive: true });
-    writeFileSync(join(repoPath, 'people/alice.md'), [
-      '---', 'type: person', 'title: Alice', '---', '', 'Alice is a founder.',
-    ].join('\n'));
-    git('git add -A && git commit -m "initial"');
-
-    // Seed: full first sync imports the anchor page + sets last_commit.
-    const { performSync } = await import('../src/commands/sync.ts');
-    await performSync(engine, { repoPath, full: true, noPull: true, noEmbed: true });
-
-    // Second commit: 101 new pages → incremental totalChanges > 100.
-    for (let i = 0; i < 101; i++) {
-      writeFileSync(join(repoPath, `notes/n${i}.md`), [
-        '---', 'type: note', `title: Note ${i}`, '---', '',
-        `[Alice](people/alice) appears in note ${i}.`,
-      ].join('\n'));
-    }
-    git('git add -A && git commit -m "add 101 pages"');
-  }, 120_000);
-
-  afterAll(async () => {
-    if (repoPath) rmSync(repoPath, { recursive: true, force: true });
-    if (engine) await engine.disconnect();
-  }, 60_000);
-
-  test('sync handler defers inline extract and queues extract{stale} follow-up; stale sweep recovers', async () => {
-    const syncHandler = (worker as unknown as { handlers: Map<string, (job: unknown) => Promise<unknown>> })
-      .handlers.get('sync');
-    expect(syncHandler).toBeDefined();
-
-    // Same payload shape the webhook submits (minus embed backfill noise).
-    const result = await syncHandler!({
-      data: { repoPath, noExtract: false, noPull: true, auto_embed_backfill: false },
-      signal: { aborted: false },
-      updateProgress: async () => {},
-    }) as { status: string; extractDeferred?: boolean; extract_stale_job_id?: number | null };
-
-    expect(result.status).toBe('synced');
-    // (a) inline extract was deferred, pages left stale.
-    expect(result.extractDeferred).toBe(true);
-    const staleBefore = await engine.countStalePagesForExtraction();
-    expect(staleBefore).toBeGreaterThan(100);
-    expect(await engine.getLinks('notes/n0')).toHaveLength(0);
-
-    // (b) a follow-up extract job with stale:true was queued.
-    expect(result.extract_stale_job_id).toBeGreaterThan(0);
-    const queue = new MinionQueue(engine);
-    const extractJobs = await queue.getJobs({ name: 'extract', limit: 5 });
-    expect(extractJobs.length).toBe(1);
-    expect((extractJobs[0].data as { stale: boolean }).stale).toBe(true);
-
-    // (c) running the extract handler's stale mode recovers: links + stamps.
-    const extractHandler = (worker as unknown as { handlers: Map<string, (job: unknown) => Promise<unknown>> })
-      .handlers.get('extract');
-    await extractHandler!({
-      data: extractJobs[0].data,
-      signal: { aborted: false },
-      updateProgress: async () => {},
-    });
-    const links = await engine.getLinks('notes/n0');
-    expect(links.some(l => l.to_slug === 'people/alice')).toBe(true);
-    const rows = await engine.executeRaw<{ links_extracted_at: string | null }>(
-      `SELECT links_extracted_at FROM pages WHERE slug = 'notes/n0'`,
-    );
-    expect(rows[0]?.links_extracted_at).not.toBeNull();
-  }, 180_000);
-
-  test('sub-threshold sync does NOT set extractDeferred (no spurious follow-up)', async () => {
-    // One more small commit → inline extract path, no deferral.
-    writeFileSync(join(repoPath, 'notes/small.md'), [
-      '---', 'type: note', 'title: Small', '---', '', 'No big deal.',
-    ].join('\n'));
-    git('git add -A && git commit -m "one small page"');
-    const { performSync } = await import('../src/commands/sync.ts');
-    const result = await performSync(engine, { repoPath, noPull: true, noEmbed: true });
-    expect(result.status).toBe('synced');
-    expect(result.extractDeferred).toBeFalsy();
-  }, 60_000);
-});

test/sync-trigger-cli.test.ts

@@ -100,10 +100,6 @@ describe('runSyncTrigger', () => {
     const job = jobs[0];
     expect(job.priority).toBe(-10);
     expect((job.data as { sourceId: string }).sourceId).toBe('default');
-    // #2849: opt in to inline extraction — the standalone sync handler
-    // defaults noExtract to TRUE, which would leave triggered syncs
-    // extraction-stale.
-    expect((job.data as { noExtract: boolean }).noExtract).toBe(false);
     expect((job.data as { auto_embed_backfill: boolean }).auto_embed_backfill).toBe(true);
   });