fix(webhook): extract links for incremental push syncs (#2849)

GitHub webhook + sync-trigger 'sync' jobs never opted into extraction:
the standalone sync handler defaults noExtract to TRUE, so webhook-
imported pages advanced the source bookmark with links_extracted_at
unstamped — and nothing behind a standalone job ever swept them (the
autopilot cycle's extract phase only walks that cycle's changedSlugs).

Fix, both halves of the issue:
- webhook + sync-trigger payloads pass noExtract:false so normal
  incremental pushes get sync's inline link/timeline extraction.
- >100-file deferral branch: performSync surfaces extractDeferred, and
  the sync job handler queues a source-scoped extract{stale:true}
  follow-up job (idempotent sweep; extract handler gains a stale mode
  backed by the same extractStaleFromDB core as `gbrain extract --stale`).

Tests: new sync-large-deferral-extract.serial.test.ts drives a real
101-file incremental sync end-to-end (deferral flag → queued follow-up →
stale sweep recovers links + watermark); webhook payload contract test +
sync-trigger noExtract assertion salvaged from #2850.

Fixes #2849
Takeover of #2850

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

docs/architecture/KEY_FILES.md

@@ -457,7 +457,6 @@ unresolvable+true|false, pre-v80 NULL/NULL rows survive).
 - `src/core/think/prompt.ts` extension — anti-bias rewrite. `withCalibration` option on `buildThinkSystemPrompt` adds anti-bias rules. `buildCalibrationBlock()` emits the `<calibration>` XML. `buildThinkUserMessage` has TWO shapes: default (question first), and with-calibration (retrieval → calibration → question) when opt-in. Wired into `runThink` via `opts.withCalibration` + `opts.calibrationHolder`.
 - `src/commands/calibration.ts` — CLI: `gbrain calibration` (read + print), `--regenerate`, `--undo-wave <ver>`, `ab-report`. MCP op `get_calibration_profile` (scope: read) backs the same data path. Source-scoped via `sourceScopeOpts(ctx)`.
 - `src/commands/serve-http.ts` extension — three admin routes: `/admin/api/calibration/profile`, `/admin/api/calibration/charts/:type` (image/svg+xml; type in {brier-trend, domain-bars, pattern-statements, abandoned-threads}), `/admin/api/calibration/pattern/:id` (drill-down).
-- `src/core/owner-holder.ts` — single source of truth for "the brain owner" holder string. `DEFAULT_OWNER_HOLDER = 'self'` (matches the consolidate facts→takes writer + `docs/takes-vs-facts.md`); `resolveOwnerHolder({override, configValue})` returns override > `emotional_weight.user_holder` config > `'self'`. Consumed by the calibration_profile cycle phase, `gbrain calibration` CLI, the `get_calibration_profile` op, `think`'s calibration block, `emotional-weight`'s `DEFAULT_USER_HOLDER`, and doctor's `calibration_freshness`. Pure; unit-tested in `test/owner-holder.test.ts`. Does NOT unify owner-identity fragmentation (`self`/`brain`/`people-<owner>`) — tracked separately.
 - `src/commands/takes.ts` extension — `gbrain takes revisit <slug>` opens $EDITOR on the source page with a `<!-- gbrain:revisit -->` cursor marker.
 - `src/commands/doctor.ts` extension — 4 checks: `abandoned_threads`, `calibration_freshness`, `grade_confidence_drift` (mitigation surface; math ships later), `voice_gate_health`.
 - `admin/src/pages/Calibration.tsx` — Calibration tab. Single-column layout. `<TrustedSVG>` wrapper handles `dangerouslySetInnerHTML` for the server-rendered SVG.

docs/takes-vs-facts.md

@@ -91,18 +91,3 @@ First full takes extraction run on a ~100K-page brain:
 4. **Self-reported ≠ verified.** "Reports 7 figures" → holder=person, weight=0.75, NOT world/1.0
 5. **No false precision.** Use 0.05 increments (0.35, 0.55, 0.75), not 0.74 or 0.82
 6. **"So what" test.** Skip Twitter handles, follower counts, obvious metadata
-
-## Owner-holder canonicalization
-
-"The brain owner" is, by convention, the holder string **`self`** — the value the
-dream `consolidate` phase stamps when it promotes the owner's hot facts into cold
-takes. Calibration, `think`, and the `doctor` calibration check resolve the owner
-holder through `resolveOwnerHolder` (`src/core/owner-holder.ts`): explicit override
-> `emotional_weight.user_holder` config > `self`.
-
-Known limitation (tracked in garrytan/gbrain#2465): the owner can also
-appear under `brain` (a take the owner asserts, via `propose_takes`) and
-`people/<owner>` (extraction that names the owner). The resolver selects the
-*default* canonical owner string for reads; it does not merge those other
-strings. Per-take attribution for other people (e.g. `people/george`) is
-unaffected and correct.

src/commands/calibration.ts

@@ -23,7 +23,6 @@ import { runPhaseCalibrationProfile } from '../core/cycle/calibration-profile.ts
 import { sourceScopeOpts, type OperationContext } from '../core/operations.ts';
 import type { GBrainConfig } from '../core/config.ts';
 import { GBrainError } from '../core/types.ts';
-import { resolveOwnerHolder } from '../core/owner-holder.ts';
 
 export interface CalibrationProfileRow {
   /** BIGSERIAL → string (postgres.js int8 wire shape; never Number() — int8
@@ -168,10 +167,7 @@ export async function runCalibration(
   config: GBrainConfig,
 ): Promise<void> {
   const { opts } = parseArgs(args);
-  const holder = resolveOwnerHolder({
-    override: opts.holder,
-    configValue: await engine.getConfig('emotional_weight.user_holder'),
-  });
+  const holder = opts.holder ?? 'garry';
   // Resolve --source / GBRAIN_SOURCE / .gbrain-source so the (now reachable, #2035)
   // calibration command targets the right source in a multi-source brain instead
   // of always reading `default`. No signal → 'default' (prior behavior).
@@ -257,15 +253,12 @@ export async function getCalibrationProfileOp(
   ctx: OperationContext,
   params: { holder?: string },
 ): Promise<CalibrationProfileRow | null> {
-  const holder = resolveOwnerHolder({
-    override: params.holder,
-    configValue: await ctx.engine.getConfig('emotional_weight.user_holder'),
-  });
+  const holder = params.holder ?? 'garry';
   if (typeof holder !== 'string' || holder.length === 0) {
     throw new GBrainError(
       'INVALID_HOLDER',
       'get_calibration_profile.holder must be a non-empty string',
-      'pass holder="<slug>" or omit to default to the owner holder (config emotional_weight.user_holder, else "self")',
+      'pass holder="<slug>" or omit to default to "garry"',
     );
   }
   const scope = sourceScopeOpts(ctx);

src/commands/doctor.ts

@@ -28,7 +28,6 @@ import type { DbUrlSource } from '../core/config.ts';
 import { gbrainPath, loadConfig } from '../core/config.ts';
 import { reflexEnabled } from '../core/context/reflex.ts';
 import { resolveSocketPath } from '../core/context/resolve-ipc.ts';
-import { resolveOwnerHolder } from '../core/owner-holder.ts';
 import { homedir } from 'os';
 import { dirname, isAbsolute, join, resolve as resolvePath } from 'path';
 import { fileURLToPath } from 'url';
@@ -1288,19 +1287,14 @@ export async function checkAbandonedThreads(engine: BrainEngine): Promise<Check>
 
 /**
  * calibration_freshness: warns when the active calibration profile is
- * older than 7 days (configurable). Default holder resolves via resolveOwnerHolder
- * (config emotional_weight.user_holder, else 'self'). Multi-source
+ * older than 7 days (configurable). Default holder 'garry'. Multi-source
  * brains see one row per source; this check uses the most recent across
  * all sources.
  */
 export async function checkCalibrationFreshness(engine: BrainEngine): Promise<Check> {
   try {
-    const ownerHolder = resolveOwnerHolder({
-      configValue: await engine.getConfig('emotional_weight.user_holder'),
-    });
     const rows = await engine.executeRaw<{ generated_at: Date | null }>(
-      `SELECT MAX(generated_at) AS generated_at FROM calibration_profiles WHERE holder = $1`,
-      [ownerHolder],
+      `SELECT MAX(generated_at) AS generated_at FROM calibration_profiles WHERE holder = 'garry'`,
     );
     const generated = rows[0]?.generated_at;
     if (!generated) {

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.
  */
-async function extractStaleFromDB(
+export async function extractStaleFromDB(
   engine: BrainEngine,
   opts: {
     dryRun: boolean;

src/commands/jobs.ts

@@ -1479,7 +1479,31 @@ export async function registerBuiltinHandlers(
       embedSkipReason = 'auto_embed_disabled';
     }
 
-    return { ...result, embed_job_id: embedJobId, embed_skip_reason: embedSkipReason };
+    // #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 };
   });
 
   registerBuiltinJob(worker, engine, 'embed', async (job) => {
@@ -1652,6 +1676,20 @@ 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/serve-http.ts

@@ -45,7 +45,6 @@ import {
   type IngestionContentType,
   type IngestionEvent,
 } from '../core/ingestion/types.ts';
-import { resolveOwnerHolder } from '../core/owner-holder.ts';
 
 /**
  * /health endpoint timeout. 3s rather than 5s: Fly.io's default
@@ -1191,7 +1190,7 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
   app.get('/admin/api/calibration/pattern/:id', requireAdmin, async (req: Request, res: Response) => {
     try {
       const { getLatestProfile } = await import('./calibration.ts');
-      const holder = resolveOwnerHolder({ override: (req.query.holder as string) || undefined, configValue: await engine.getConfig('emotional_weight.user_holder') });
+      const holder = (req.query.holder as string) || 'garry';
       const profile = await getLatestProfile(engine, { holder });
       if (!profile) {
         res.status(404).json({ error: 'no_profile' });
@@ -1241,7 +1240,7 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
   app.get('/admin/api/calibration/profile', requireAdmin, async (req: Request, res: Response) => {
     try {
       const { getLatestProfile } = await import('./calibration.ts');
-      const holder = resolveOwnerHolder({ override: (req.query.holder as string) || undefined, configValue: await engine.getConfig('emotional_weight.user_holder') });
+      const holder = (req.query.holder as string) || 'garry';
       const profile = await getLatestProfile(engine, { holder });
       res.json(profile);
     } catch (err) {
@@ -1258,7 +1257,7 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
         renderAbandonedThreadsCard,
         renderPatternStatementsCard,
       } = await import('../core/calibration/svg-renderer.ts');
-      const holder = resolveOwnerHolder({ override: (req.query.holder as string) || undefined, configValue: await engine.getConfig('emotional_weight.user_holder') });
+      const holder = (req.query.holder as string) || 'garry';
       const type = req.params.type;
       const profile = await getLatestProfile(engine, { holder });
 
@@ -2147,8 +2146,13 @@ 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 auto_embed_backfill=true and priority -10
-  //     (above autopilot's 0).
+  // 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.
   // ---------------------------------------------------------------------------
   const githubWebhookLimiter = rateLimit({
     windowMs: 60_000,
@@ -2268,6 +2272,7 @@ 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

@@ -222,6 +222,14 @@ 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;
 }
 
 /**
@@ -1379,6 +1387,10 @@ 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',
     },
@@ -3287,11 +3299,16 @@ 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}` : ''}' ` +
-      `(or let the autopilot cycle's extract phase sweep it).`,
+      `(sync jobs queue this follow-up automatically).`,
     );
   }
   if (!opts.noExtract && totalChanges <= 100 && pagesAffected.length > 0) {
@@ -3400,6 +3417,7 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
     chunksCreated,
     embedded,
     pagesAffected,
+    extractDeferred,
   };
 }
 

src/commands/takes.ts

@@ -29,7 +29,6 @@ import {
 } from '../core/takes-fence.ts';
 import { withPageLock } from '../core/page-lock.ts';
 import { resolveSourceId } from '../core/source-resolver.ts';
-import { resolveOwnerHolder } from '../core/owner-holder.ts';
 
 // --- Helpers ---
 
@@ -365,7 +364,7 @@ async function cmdResolve(engine: BrainEngine, args: string[], sourceId?: string
   // --evidence is the v0.30.0 alias for --source on the resolve subcommand
   // (semantic clarity: "what evidence resolved this bet?").
   const source = flagValue(args, '--evidence') ?? flagValue(args, '--source');
-  const resolvedBy = flagValue(args, '--by') ?? resolveOwnerHolder({ configValue: await engine.getConfig('emotional_weight.user_holder') });
+  const resolvedBy = flagValue(args, '--by') ?? 'garry';
   const dirArg = flagValue(args, '--dir');
 
   const pageId = await getPageId(engine, slug, sourceId);

src/core/brainstorm/orchestrator.ts

@@ -68,7 +68,6 @@ import {
   type BrainstormCheckpoint,
   type CheckpointCross,
 } from './checkpoint.ts';
-import { resolveOwnerHolder } from '../owner-holder.ts';
 
 export { BudgetExhausted };
 
@@ -140,7 +139,7 @@ export interface BrainstormOptions {
   modelOverride?: string;
   /** Skip the cost-preview TTY grace window. Required for non-interactive callers. */
   skipCostPreview?: boolean;
-  /** When set, force the user holder for calibration profile lookup. Falls back to config (`emotional_weight.user_holder`) then `'self'`. */
+  /** When set, force the user holder for calibration profile lookup. Falls back to config (`emotional_weight.user_holder`) then `'garry'`. */
   holderOverride?: string;
   /** Source scope. */
   sourceId?: string;
@@ -624,7 +623,7 @@ async function _runBrainstormInner(
   }
 
   // ---- Phase 3: calibration context (cold-start fallback) ----
-  const holder = resolveOwnerHolder({ override: opts.holderOverride, configValue: config.emotional_weight?.user_holder });
+  const holder = opts.holderOverride ?? config.emotional_weight?.user_holder ?? 'garry';
   const calibContext = await loadCalibrationContext(engine, {
     holder,
     sourceId: opts.sourceId,

src/core/calibration/think-ab.ts

@@ -25,7 +25,7 @@ import type { BrainEngine } from '../engine.ts';
 
 export interface ABRunInput {
   question: string;
-  /** Holder context for calibration. Resolves via resolveOwnerHolder (config emotional_weight.user_holder, else 'self'). */
+  /** Holder context for calibration. Default 'garry'. */
   holder?: string;
   /** Engine for DB write. */
   engine: BrainEngine;

src/core/cycle/calibration-profile.ts

@@ -26,7 +26,6 @@
  */
 
 import { BaseCyclePhase, type ScopedReadOpts, type BasePhaseOpts } from './base-phase.ts';
-import { resolveOwnerHolder } from '../owner-holder.ts';
 import { chat as gatewayChat } from '../ai/gateway.ts';
 import { TIER_DEFAULTS } from '../model-config.ts';
 import { gateVoice, type VoiceGateGenerator, type VoiceGateJudge } from '../calibration/voice-gate.ts';
@@ -97,7 +96,7 @@ export type PatternStatementsGenerator = (input: {
 export type BiasTagsGenerator = (patterns: string[]) => Promise<string[]>;
 
 export interface CalibrationProfileOpts extends BasePhaseOpts {
-  /** Holder to generate the profile for. Default resolves via resolveOwnerHolder (config emotional_weight.user_holder, else 'self'). */
+  /** Holder to generate the profile for. Default 'garry'. */
   holder?: string;
   /** Inject the patterns generator (tests). */
   patternsGenerator?: PatternStatementsGenerator;
@@ -228,10 +227,7 @@ class CalibrationProfilePhase extends BaseCyclePhase {
     _ctx: OperationContext,
     opts: CalibrationProfileOpts,
   ): Promise<{ summary: string; details: Record<string, unknown>; status?: PhaseStatus }> {
-    const holder = resolveOwnerHolder({
-      override: opts.holder,
-      configValue: await engine.getConfig('emotional_weight.user_holder'),
-    });
+    const holder = opts.holder ?? 'garry';
     const promptVersion = opts.promptVersion ?? CALIBRATION_PROFILE_PROMPT_VERSION;
     const modelId = opts.model ?? TIER_DEFAULTS.reasoning;
     const gradeCompletion = opts.gradeCompletion ?? 1.0;

src/core/cycle/emotional-weight.ts

@@ -14,8 +14,6 @@
  * See `loadHighEmotionTags` for the resolution path.
  */
 
-import { DEFAULT_OWNER_HOLDER } from '../owner-holder.ts';
-
 /**
  * Default high-emotion tag seed list. Pages with any tag in this set get the
  * tag-emotion boost in the formula below. Override via config key
@@ -45,12 +43,11 @@ export const HIGH_EMOTION_TAGS: ReadonlySet<string> = new Set([
 ]);
 
 /**
- * Holder name treated as "the user" for the user-as-holder ratio. Configurable
- * via the `emotional_weight.user_holder` config key; defaults to the canonical
- * owner holder ('self', DEFAULT_OWNER_HOLDER) so it matches the consolidate
- * facts→takes writer instead of a hardcoded name.
+ * Holder name treated as "the user" for the Garry-as-holder ratio. Configurable
+ * via the `emotional_weight.user_holder` config key (defaults to 'garry' to
+ * match the v0.28 schema's takes table convention).
  */
-export const DEFAULT_USER_HOLDER = DEFAULT_OWNER_HOLDER;
+export const DEFAULT_USER_HOLDER = 'garry';
 
 export interface EmotionalWeightTake {
   holder: string;

src/core/operations.ts

@@ -3289,7 +3289,7 @@ const get_calibration_profile: Operation = {
     holder: {
       type: 'string',
       description:
-        "Holder slug, e.g. 'self' or 'people/charlie-example'. Defaults to config emotional_weight.user_holder, else 'self', when omitted.",
+        "Holder slug, e.g. 'garry' or 'people/charlie-example'. Defaults to 'garry' when omitted.",
     },
   },
   handler: async (ctx, p) => {

src/core/owner-holder.ts

@@ -1,24 +0,0 @@
-/**
- * Canonical holder string for "the brain owner," resolved in ONE place so the
- * calibration / think / doctor / emotional-weight defaults stop disagreeing.
- *
- * The default matches the consolidate facts→takes writer
- * (src/core/cycle/phases/consolidate.ts: holder:'self') and docs/takes-vs-facts.md.
- * Do NOT introduce a fourth literal — three already exist historically
- * ('garry', 'system', 'self'); this is the source of truth.
- *
- * NORMALIZATION NOTE: the brain owner may also appear under other holder
- * strings — 'brain' (propose_takes when the author asserts a claim) and
- * people/<owner> (extraction that names the owner). This resolver only selects
- * the *default* canonical owner string for reads; it does NOT merge those other
- * strings. Unifying them is owner-identity entity-resolution, tracked separately
- * (see garrytan/gbrain#2465). Until then, historical owner takes
- * under 'brain'/people-<owner> are not folded into the default profile.
- */
-export const DEFAULT_OWNER_HOLDER = 'self';
-
-export function resolveOwnerHolder(
-  opts: { override?: string | null; configValue?: string | null },
-): string {
-  return opts.override ?? opts.configValue ?? DEFAULT_OWNER_HOLDER;
-}

src/core/think/index.ts

@@ -23,7 +23,6 @@ import { runGather, renderPagesBlock, takesHitToTakeForPrompt } from './gather.t
 import { renderTakesBlock } from './sanitize.ts';
 import { buildThinkSystemPrompt, buildThinkUserMessage } from './prompt.ts';
 import { resolveCitations, type ParsedCitation } from './cite-render.ts';
-import { resolveOwnerHolder } from '../owner-holder.ts';
 import { resolveModel } from '../model-config.ts';
 import { chat as gatewayChat, probeChatModel, type ChatResult } from '../ai/gateway.ts';
 import { AIConfigError } from '../ai/errors.ts';
@@ -77,8 +76,8 @@ export interface RunThinkOpts {
    */
   withCalibration?: boolean;
   /**
-   * Holder to retrieve the calibration profile for. Resolves via resolveOwnerHolder
-   * (config emotional_weight.user_holder, else 'self'). Only consulted when withCalibration=true.
+   * Holder to retrieve the calibration profile for. Default 'garry'. Only
+   * consulted when withCalibration=true.
    */
   calibrationHolder?: string;
   /**
@@ -309,10 +308,7 @@ export async function runThink(
     try {
       const { getLatestProfile } = await import('../../commands/calibration.ts');
       const profile = await getLatestProfile(engine, {
-        holder: resolveOwnerHolder({
-          override: opts.calibrationHolder,
-          configValue: await engine.getConfig('emotional_weight.user_holder'),
-        }),
+        holder: opts.calibrationHolder ?? 'garry',
       });
       if (profile) {
         calibrationBlockOpts = {

test/calibration-cli.test.ts

@@ -27,12 +27,6 @@ function buildMockEngine(opts: { rows: CalibrationProfileRow[] }): {
   const capturedParams: unknown[][] = [];
   const engine = {
     kind: 'pglite',
-    // #2464: getCalibrationProfileOp resolves the owner holder via
-    // resolveOwnerHolder(config emotional_weight.user_holder, else 'self'), so the
-    // mock must implement getConfig. null = key unset → resolver falls back to 'self'.
-    async getConfig(): Promise<string | null> {
-      return null;
-    },
     async executeRaw<T>(sql: string, params?: unknown[]): Promise<T[]> {
       capturedSql.push(sql);
       capturedParams.push(params ?? []);
@@ -217,17 +211,17 @@ describe('formatProfileText', () => {
 // ─── getCalibrationProfileOp ────────────────────────────────────────
 
 describe('getCalibrationProfileOp (MCP)', () => {
-  test('defaults holder to "self" when omitted (config emotional_weight.user_holder unset)', async () => {
-    const { engine } = buildMockEngine({ rows: [buildProfile({ holder: 'self' })] });
+  test('defaults holder to "garry" when omitted', async () => {
+    const { engine } = buildMockEngine({ rows: [buildProfile({ holder: 'garry' })] });
     const ctx = buildCtx(engine);
     const result = await getCalibrationProfileOp(ctx, {});
-    expect(result?.holder).toBe('self');
+    expect(result?.holder).toBe('garry');
   });
 
   test('routes through sourceScopeOpts: scalar source-bound client gets source-scoped result', async () => {
     const rows = [
-      buildProfile({ holder: 'self', source_id: 'default' }),
-      buildProfile({ holder: 'self', source_id: 'tenant-b' }),
+      buildProfile({ holder: 'garry', source_id: 'default' }),
+      buildProfile({ holder: 'garry', source_id: 'tenant-b' }),
     ];
     const { engine } = buildMockEngine({ rows });
     const ctx = buildCtx(engine, { sourceId: 'tenant-b' });
@@ -237,8 +231,8 @@ describe('getCalibrationProfileOp (MCP)', () => {
 
   test('federated read scope sees the union of allowed sources', async () => {
     const rows = [
-      buildProfile({ holder: 'self', source_id: 'tenant-a' }),
-      buildProfile({ holder: 'self', source_id: 'tenant-z' }),
+      buildProfile({ holder: 'garry', source_id: 'tenant-a' }),
+      buildProfile({ holder: 'garry', source_id: 'tenant-z' }),
     ];
     const { engine } = buildMockEngine({ rows });
     const ctx = buildCtx(engine, { allowedSources: ['tenant-a', 'tenant-b'] });

test/calibration-profile.test.ts

@@ -32,7 +32,7 @@ interface CapturedSql {
   params: unknown[];
 }
 
-function buildMockEngine(opts: { scorecard: TakesScorecard; userHolder?: string | null }): {
+function buildMockEngine(opts: { scorecard: TakesScorecard }): {
   engine: BrainEngine;
   captured: CapturedSql[];
 } {
@@ -42,10 +42,6 @@ function buildMockEngine(opts: { scorecard: TakesScorecard; userHolder?: string
     async getScorecard() {
       return opts.scorecard;
     },
-    async getConfig(key: string): Promise<string | null> {
-      if (key === 'emotional_weight.user_holder') return opts.userHolder ?? null;
-      return null;
-    },
     async executeRaw<T>(sql: string, params?: unknown[]): Promise<T[]> {
       captured.push({ sql, params: params ?? [] });
       return [];
@@ -238,7 +234,7 @@ describe('runPhaseCalibrationProfile — phase integration', () => {
     // grade_completion, domain_scorecards_json, patterns[], voice_passed, voice_attempts,
     // bias_tags[], model_id
     expect(insert!.params[0]).toBe('default'); // source_id
-    expect(insert!.params[1]).toBe('self'); // holder (resolved via resolveOwnerHolder, no override)
+    expect(insert!.params[1]).toBe('garry'); // holder
     expect(insert!.params[2]).toBe(12); // total_resolved
     expect(insert!.params[9]).toBe(true); // voice_gate_passed
     expect(insert!.params[10]).toBe(1); // voice_gate_attempts
@@ -334,24 +330,4 @@ describe('runPhaseCalibrationProfile — phase integration', () => {
     const insert = captured.find(c => c.sql.includes('INSERT INTO calibration_profiles'));
     expect(insert!.params[0]).toBe('tenant-b');
   });
-
-  test('cold-brain summary uses resolved owner holder self when user_holder unset', async () => {
-    const { engine } = buildMockEngine({
-      scorecard: { total_bets: 0, resolved: 0, correct: 0, incorrect: 0, partial: 0,
-        accuracy: null, brier: null, partial_rate: null, unresolvable_count: 0, unresolvable_rate: null },
-    });
-    const result = await runPhaseCalibrationProfile(buildCtx(engine), {});
-    expect(result.summary).toContain('holder=self');
-    expect(result.summary).not.toContain('holder=garry');
-  });
-
-  test('configured user_holder overrides the default in the cold-brain summary', async () => {
-    const { engine } = buildMockEngine({
-      scorecard: { total_bets: 0, resolved: 0, correct: 0, incorrect: 0, partial: 0,
-        accuracy: null, brier: null, partial_rate: null, unresolvable_count: 0, unresolvable_rate: null },
-      userHolder: 'people/charlie-example',
-    });
-    const result = await runPhaseCalibrationProfile(buildCtx(engine), {});
-    expect(result.summary).toContain('holder=people/charlie-example');
-  });
 });

test/doctor-calibration-checks.test.ts

@@ -32,12 +32,6 @@ function buildMockEngine(opts: {
 }): BrainEngine {
   return {
     kind: 'pglite',
-    // #2464: checkCalibrationFreshness resolves the owner holder via
-    // resolveOwnerHolder(config emotional_weight.user_holder, else 'self'), so the
-    // mock must implement getConfig. null = key unset → resolver falls back to 'self'.
-    async getConfig(): Promise<string | null> {
-      return null;
-    },
     async executeRaw<T>(sql: string): Promise<T[]> {
       if (opts.throwOn && opts.throwOn.test(sql)) {
         throw new Error('mock engine error: ' + sql.slice(0, 50));

test/emotional-weight.test.ts

@@ -112,7 +112,3 @@ describe('computeEmotionalWeight', () => {
     expect(HIGH_EMOTION_TAGS.has('mental-health')).toBe(true);
   });
 });
-
-test('DEFAULT_USER_HOLDER is the canonical owner holder self', () => {
-  expect(DEFAULT_USER_HOLDER).toBe('self');
-});

test/owner-holder.test.ts

@@ -1,27 +0,0 @@
-import { describe, test, expect } from 'bun:test';
-import { resolveOwnerHolder, DEFAULT_OWNER_HOLDER } from '../src/core/owner-holder.ts';
-
-describe('owner-holder', () => {
-  test('DEFAULT_OWNER_HOLDER is self', () => {
-    expect(DEFAULT_OWNER_HOLDER).toBe('self');
-  });
-
-  test('defaults to self when nothing provided', () => {
-    expect(resolveOwnerHolder({})).toBe('self');
-  });
-
-  test('null/undefined config falls back to self', () => {
-    expect(resolveOwnerHolder({ configValue: null })).toBe('self');
-    expect(resolveOwnerHolder({ configValue: undefined })).toBe('self');
-  });
-
-  test('uses config value when set and no override', () => {
-    expect(resolveOwnerHolder({ configValue: 'people/charlie-example' }))
-      .toBe('people/charlie-example');
-  });
-
-  test('override beats config and default', () => {
-    expect(resolveOwnerHolder({ override: 'world', configValue: 'people/charlie-example' }))
-      .toBe('world');
-  });
-});

test/sources-webhook.test.ts

@@ -16,6 +16,7 @@
  */
 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';
@@ -123,3 +124,25 @@ 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

@@ -0,0 +1,130 @@
+/**
+ * #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

@@ -100,6 +100,10 @@ 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);
   });