fix(reference): route exit codes through setCliExitVerdict; use withEnv in e2e test

CI red on two guards:
- test/cli-exit-verdict-pin.test.ts: raw process.exitCode writes in
  src/commands/reference.ts -> replaced with setCliExitVerdict.
- check:test-isolation R1: direct process.env.GBRAIN_SOURCE mutation in
  test/reference-flag.test.ts -> wrapped the two runReference calls in
  withEnv({ GBRAIN_SOURCE: undefined }).

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

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.

skills/article-enrichment/SKILL.md

@@ -85,6 +85,10 @@ gbrain get media/articles/<slug>
 
 # 5. Cross-link entities
 #    For every person/company mentioned, add a timeline back-link.
+#    Mark NEW pages minted for article subjects the reader only reads ABOUT
+#    (not personal contacts) as reference: `gbrain reference <slug>`
+#    (or reference: true in frontmatter). Exempts them from coverage nudges;
+#    they stay searchable. Default for real contacts: do NOT set it.
 ```
 
 ## Quality bar

skills/book-mirror/SKILL.md

@@ -273,6 +273,13 @@ Cross-link entities mentioned in the analysis:
 - For every person the right column references with a brain page, add a
   back-link from `people/<slug>` to the new `media/books/<slug>-personalized`
   page (per `conventions/quality.md` Iron Law).
+- **Mark book figures as reference entities.** Any NEW person/company page you
+  mint for a figure from the book (an author, a historical figure, a company
+  the book discusses) — someone the reader reads ABOUT but doesn't personally
+  interact with — should be flagged: `gbrain reference <slug>` (or
+  `reference: true` in frontmatter). They stay fully searchable/linkable but
+  are exempt from coverage nudges (timeline/links). Skip this for anyone the
+  reader actually knows. Default for normal contacts: do NOT set it.
 
 ## Quality bar (the bar)
 

skills/conventions/reference-entities.md

@@ -0,0 +1,62 @@
+# Convention: Reference entities (canon figures)
+
+Some person/company pages are people/orgs the user **reads about** but does not
+personally interact with — a book's author, a historical figure, a company an
+article discusses (Andy Grove, Kleiner Perkins, Intel…). They are real
+knowledge, worth a page, but they have **no dated history in the user's own
+life**, so the entity coverage metrics (`timeline_coverage`,
+`entity_link_coverage`) flag them as permanently incomplete with no honest fix.
+
+The `reference: true` frontmatter flag resolves this.
+
+## What it does
+
+- A page with `reference: true` is **exempt from the entity coverage metrics
+  only** (`timeline_coverage`, `entity_link_coverage`, and their onboard
+  nudges).
+- It keeps its real `type` (`person` / `company`), so it stays **fully
+  searchable, enrichable, linkable, and edge-resolvable**. NOTHING about
+  retrieval changes — this is the whole reason it's a flag, not a new `type`.
+- It is **opt-in**. Absent / `false` / anything-but-`true` = a normal entity
+  that DOES count toward coverage. **This is the default — do not set it on real
+  contacts.**
+
+## When to set it
+
+Set `reference: true` when the entity is a figure/org the user reads ABOUT, not
+someone they deal with:
+
+- authors and figures discussed in a book (book-mirror) or article
+  (article-enrichment)
+- historical / canon figures imported as reference knowledge
+- companies named only as examples in source material
+
+Do NOT set it for people the user actually meets, emails, or works with — those
+are normal entities whose missing timeline/links is a real, actionable gap.
+
+## How to set it
+
+```bash
+gbrain reference <slug>            # mark as reference
+gbrain reference <slug> --unset    # back to a normal entity
+```
+
+The command writes the flag to BOTH the markdown frontmatter (durable; survives
+re-ingest / engine rebuild — markdown is the source of truth) AND the engine
+JSONB (so coverage reflects it immediately, no re-sync). It's idempotent. You
+can also hand-edit frontmatter (`reference: true`) and re-ingest.
+
+## Why a flag, not a type
+
+A new `type: reference-person` would drop the page out of every
+`type IN ('person','company')` filter — search, enrichment, whoknows, link
+inference — so you'd lose the figure everywhere, not just the metric. The flag
+narrows the change to exactly the coverage denominators and nothing else.
+
+## Implementation
+
+`src/core/reference-flag.ts` — `referenceExclusionSql(alias?)` is the single
+source of truth for the predicate `(frontmatter->>'reference') IS DISTINCT FROM
+'true'`, ANDed into both numerator and denominator at every coverage site
+(getHealth in both engines, onboard/checks.ts, init-nudge.ts). Backed by the GIN
+index on `pages.frontmatter`.

skills/enrich/SKILL.md

@@ -268,6 +268,18 @@ Active items, pending decisions, things to track.
 - **YYYY-MM-DD** | Event description [Source: ...]
 ```
 
+### Reference entities (canon figures)
+
+If the entity is someone/something the user reads ABOUT but does not personally
+interact with — a book author, a historical figure, a company discussed in an
+article — mark the page as reference: `gbrain reference <slug>` (or
+`reference: true` in frontmatter). Reference pages keep their `person`/`company`
+type and stay fully searchable, enrichable, and linkable; they are only exempt
+from the entity coverage nudges (timeline/links) that don't apply to figures
+with no dated history in the user's own life. **Default: do NOT set it** — real
+people and companies the user deals with are normal entities. Full convention:
+`conventions/reference-entities.md`.
+
 ### Step 7: Cross-reference
 
 - Update company pages from person enrichment (and vice versa)

skills/maintain/SKILL.md

@@ -270,6 +270,11 @@ Populate them periodically or after major imports:
 - `gbrain stats` — verify `link_count > 0` and `timeline_entry_count > 0` after extraction.
 - `gbrain health` — review `link_coverage` and `timeline_coverage` percentages
   on entity pages (person/company). Below 50% means more extraction is needed.
+  Note: pages flagged `reference: true` (canon/reference figures the user only
+  reads about) are EXEMPT from these two metrics — if coverage looks stuck
+  because of book/article-imported figures with no real history, mark them with
+  `gbrain reference <slug>` rather than chasing the percentage. See
+  `conventions/reference-entities.md`.
 
 Available link types (use with `gbrain graph-query --type`):
 `attended`, `works_at`, `invested_in`, `founded`, `advises`, `mentions`, `source`.

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', 'reference', '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']);
 // 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.
@@ -1652,6 +1652,11 @@ async function handleCliOnly(command: string, args: string[]) {
         await runFiles(engine, args);
         break;
       }
+      case 'reference': {
+        const { runReference } = await import('./commands/reference.ts');
+        await runReference(engine, args);
+        break;
+      }
       case 'embed': {
         const { runEmbed } = await import('./commands/embed.ts');
         await runEmbed(engine, args);

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/reference.ts

@@ -0,0 +1,130 @@
+// gbrain reference <slug> [--unset] [--brain <dir>] [--json]
+//
+// Mark (or unmark) a page as a reference-only entity. A reference page keeps its
+// real type (person/company) — fully searchable/enrichable/linkable — but is
+// exempt from the entity coverage metrics (timeline_coverage,
+// entity_link_coverage). See src/core/reference-flag.ts for the rationale.
+//
+// Durability: the flag is written to BOTH the markdown frontmatter (source of
+// truth; survives re-ingest / engine rebuild) AND the engine `pages.frontmatter`
+// JSONB (so the metric reflects it immediately, no re-sync needed).
+
+import { existsSync, readFileSync, writeFileSync } from 'node:fs';
+import { isAbsolute, join, resolve } from 'node:path';
+import { setCliExitVerdict } from '../core/cli-force-exit.ts';
+import type { BrainEngine } from '../core/engine.ts';
+import { REFERENCE_FRONTMATTER_KEY } from '../core/reference-flag.ts';
+import { resolveSourceId } from '../core/source-resolver.ts';
+
+/** Insert/replace/remove `reference: true` in a markdown frontmatter block.
+ *  Minimal-diff: only the one line changes; key order is otherwise preserved. */
+export function applyReferenceFrontmatter(content: string, on: boolean): string {
+  const keyLine = `${REFERENCE_FRONTMATTER_KEY}: true`;
+  const block = content.match(/^---\n([\s\S]*?)\n---/);
+
+  if (!block) {
+    // No frontmatter. Nothing to remove; if setting, prepend a block.
+    if (!on) return content;
+    return `---\n${keyLine}\n---\n\n${content}`;
+  }
+
+  let fm = block[1];
+  const hasKey = new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$`, 'm').test(fm);
+
+  if (on) {
+    fm = hasKey
+      ? fm.replace(new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$`, 'm'), keyLine)
+      : `${fm}\n${keyLine}`;
+  } else {
+    if (!hasKey) return content;
+    fm = fm.replace(new RegExp(`^${REFERENCE_FRONTMATTER_KEY}:.*$\\n?`, 'm'), '');
+  }
+
+  // Function replacement so YAML chars ($, & …) in fm aren't treated as
+  // replacement patterns.
+  return content.replace(/^---\n[\s\S]*?\n---/, () => `---\n${fm}\n---`);
+}
+
+function parseArgs(args: string[]): { slug?: string; unset: boolean; json: boolean; brain?: string; source?: string } {
+  let slug: string | undefined;
+  let unset = false;
+  let json = false;
+  let brain: string | undefined;
+  let source: string | undefined;
+  for (let i = 0; i < args.length; i++) {
+    const a = args[i];
+    if (a === '--unset') unset = true;
+    else if (a === '--json') json = true;
+    else if (a === '--brain' || a === '--dir') brain = args[++i];
+    else if (a === '--source') source = args[++i];
+    else if (!a.startsWith('--') && !slug) slug = a;
+  }
+  return { slug, unset, json, brain, source };
+}
+
+async function resolveBrainDir(engine: BrainEngine, explicit?: string): Promise<string | null> {
+  if (explicit) return resolve(explicit);
+  const configured = await engine.getConfig('sync.repo_path');
+  if (configured && existsSync(configured)) return resolve(configured);
+  return null;
+}
+
+export async function runReference(engine: BrainEngine, args: string[]): Promise<void> {
+  const { slug, unset, json, brain, source } = parseArgs(args);
+  if (!slug) {
+    console.error('Usage: gbrain reference <slug> [--unset] [--source <id>] [--brain <dir>] [--json]');
+    setCliExitVerdict(2);
+    return;
+  }
+
+  const brainDir = await resolveBrainDir(engine, brain);
+  if (!brainDir) {
+    console.error('reference: could not resolve brain dir. Pass --brain <dir> or set sync.repo_path.');
+    setCliExitVerdict(1);
+    return;
+  }
+
+  const rel = slug.endsWith('.md') ? slug : `${slug}.md`;
+  const filePath = isAbsolute(rel) ? rel : join(brainDir, rel);
+  if (!existsSync(filePath)) {
+    console.error(`reference: page not found on disk: ${filePath}`);
+    setCliExitVerdict(1);
+    return;
+  }
+
+  // 1) Durable: edit the markdown frontmatter.
+  const before = readFileSync(filePath, 'utf8');
+  const after = applyReferenceFrontmatter(before, !unset);
+  const fileChanged = after !== before;
+  if (fileChanged) writeFileSync(filePath, after, 'utf8');
+
+  // 2) Immediate: update the engine frontmatter JSONB so the metric reflects it
+  //    without waiting for a re-sync. Scoped to (source_id, slug) — slug is only
+  //    unique per source, so a bare-slug UPDATE would clobber same-named pages
+  //    in every other source. Resolve the source from the brain dir (tier-4
+  //    local_path match) unless --source / GBRAIN_SOURCE overrides.
+  const cleanSlug = slug.replace(/\.md$/, '');
+  const sourceId = await resolveSourceId(engine, source ?? null, brainDir);
+  if (unset) {
+    await engine.executeRaw(
+      `UPDATE pages SET frontmatter = frontmatter - '${REFERENCE_FRONTMATTER_KEY}' WHERE slug = $1 AND source_id = $2`,
+      [cleanSlug, sourceId],
+    );
+  } else {
+    await engine.executeRaw(
+      `UPDATE pages SET frontmatter = jsonb_set(COALESCE(frontmatter, '{}'::jsonb), '{${REFERENCE_FRONTMATTER_KEY}}', 'true'::jsonb) WHERE slug = $1 AND source_id = $2`,
+      [cleanSlug, sourceId],
+    );
+  }
+
+  const result = { slug: cleanSlug, source_id: sourceId, reference: !unset, file_changed: fileChanged, file: filePath };
+  if (json) {
+    console.log(JSON.stringify(result));
+  } else {
+    const verb = unset ? 'unmarked' : 'marked';
+    console.log(`${verb} ${cleanSlug} as reference=${!unset}${fileChanged ? '' : ' (frontmatter already current)'}`);
+    if (!unset) {
+      console.log('  → exempt from timeline_coverage / entity_link_coverage; still fully searchable & linkable.');
+    }
+  }
+}

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 });
 

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/onboard/checks.ts

@@ -18,6 +18,7 @@
 import type { BrainEngine } from '../engine.ts';
 import type { RemediationStep } from '../remediation-step.ts';
 import { makeRemediationStep } from '../remediation-step.ts';
+import { referenceExclusionSql } from '../reference-flag.ts';
 
 /** Shared shape returned by all four checks. */
 export interface OnboardCheckResult {
@@ -120,7 +121,8 @@ export async function checkEntityLinkCoverage(
     engine,
     `SELECT COUNT(*) AS count FROM pages
        WHERE type IN ('person', 'company', 'organization', 'entity')
-         AND deleted_at IS NULL`,
+         AND deleted_at IS NULL
+         AND ${referenceExclusionSql()}`,
   );
 
   if (totalEntities === 0) {
@@ -144,6 +146,7 @@ export async function checkEntityLinkCoverage(
        SELECT p.id FROM pages p ${sampleClause}
        WHERE p.type IN ('person', 'company', 'organization', 'entity')
          AND p.deleted_at IS NULL
+         AND ${referenceExclusionSql('p')}
          AND EXISTS (SELECT 1 FROM links l WHERE l.to_page_id = p.id)
      ) sub`,
   );
@@ -215,7 +218,8 @@ export async function checkTimelineCoverage(
     engine,
     `SELECT COUNT(*) AS count FROM pages
        WHERE type IN ('person', 'company', 'organization', 'entity')
-         AND deleted_at IS NULL`,
+         AND deleted_at IS NULL
+         AND ${referenceExclusionSql()}`,
   );
 
   if (totalEntities === 0) {
@@ -237,6 +241,7 @@ export async function checkTimelineCoverage(
        SELECT p.id FROM pages p ${sampleClause}
        WHERE p.type IN ('person', 'company', 'organization', 'entity')
          AND p.deleted_at IS NULL
+         AND ${referenceExclusionSql('p')}
          AND EXISTS (SELECT 1 FROM timeline_entries t WHERE t.page_id = p.id)
      ) sub`,
   );

src/core/onboard/init-nudge.ts

@@ -14,6 +14,7 @@
 // also short-circuits (CI/scripted callers see nothing).
 
 import type { BrainEngine } from '../engine.ts';
+import { referenceExclusionSql } from '../reference-flag.ts';
 
 const NUDGE_BUDGET_MS = 3000;
 
@@ -57,7 +58,8 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
       engine.executeRaw<{ count: string | number }>(
         `SELECT COUNT(*) AS count FROM pages
            WHERE type IN ('person', 'company', 'organization', 'entity')
-             AND deleted_at IS NULL`,
+             AND deleted_at IS NULL
+             AND ${referenceExclusionSql()}`,
         [],
         { signal: controller.signal },
       ),
@@ -65,6 +67,7 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
         `SELECT COUNT(*) AS count FROM pages p
            WHERE p.type IN ('person', 'company', 'organization', 'entity')
              AND p.deleted_at IS NULL
+             AND ${referenceExclusionSql('p')}
              AND EXISTS (SELECT 1 FROM links l WHERE l.to_page_id = p.id)`,
         [],
         { signal: controller.signal },
@@ -73,6 +76,7 @@ export async function runInitNudge(engine: BrainEngine): Promise<void> {
         `SELECT COUNT(*) AS count FROM pages p
            WHERE p.type IN ('person', 'company', 'organization', 'entity')
              AND p.deleted_at IS NULL
+             AND ${referenceExclusionSql('p')}
              AND EXISTS (SELECT 1 FROM timeline_entries t WHERE t.page_id = p.id)`,
         [],
         { signal: controller.signal },

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/pglite-engine.ts

@@ -23,6 +23,7 @@ import { runMigrations } from './migrate.ts';
 import { PGLITE_SCHEMA_SQL, getPGLiteSchema } from './pglite-schema.ts';
 import { DEFAULT_EMBEDDING_MODEL, DEFAULT_EMBEDDING_DIMENSIONS } from './ai/defaults.ts';
 import { DELETE_BATCH_SIZE } from './engine-constants.ts';
+import { referenceExclusionSql } from './reference-flag.ts';
 import { MARKDOWN_CHUNKER_VERSION } from './chunkers/recursive.ts';
 import { acquireLock, releaseLock, type LockHandle } from './pglite-lock.ts';
 import { getFtsLanguage } from './fts-language.ts';
@@ -5202,6 +5203,7 @@ export class PGLiteEngine implements BrainEngine {
     const { rows: [h] } = await this.db.query(`
       WITH entity_pages AS (
         SELECT id, slug FROM pages WHERE type IN ('person', 'company')
+          AND ${referenceExclusionSql()}
       )
       SELECT
         (SELECT count(*) FROM pages) as page_count,

src/core/postgres-engine.ts

@@ -5320,7 +5320,12 @@ export class PostgresEngine implements BrainEngine {
     // is working as intended, not an orphan.
     const [h] = await sql`
       WITH entity_pages AS (
+        -- reference:true pages are exempt from coverage metrics.
+        -- Inlined (postgres.js tagged-template interpolation = bound param,
+        -- not raw SQL); keep in sync with referenceExclusionSql() in
+        -- reference-flag.ts.
         SELECT id, slug FROM pages WHERE type IN ('person', 'company')
+          AND (frontmatter->>'reference') IS DISTINCT FROM 'true'
       )
       SELECT
         (SELECT count(*) FROM pages) as page_count,

src/core/reference-flag.ts

@@ -0,0 +1,37 @@
+// Reference / canon entities.
+//
+// A page with frontmatter `reference: true` is a reference-only entity — a
+// figure or organization imported from a book / article / external source that
+// the user reads ABOUT but does not actively interact with (e.g. Andy Grove,
+// Kleiner Perkins). It keeps its real `type` (`person` / `company`), so it stays
+// fully searchable, enrichable, linkable, and edge-resolvable — NOTHING about
+// retrieval changes.
+//
+// The ONLY behavior it opts out of is the entity *coverage* metrics
+// (`timeline_coverage`, `entity_link_coverage` + their onboard-nudge mirrors).
+// Those metrics nudge "this entity should accumulate dated history / inbound
+// links"; that assumption is right for people you actually deal with and wrong
+// for canon imports, which have no dated events in the user's life. Excluding
+// them keeps the metric honest and actionable instead of permanently red.
+//
+// Opt-in: absent / false / anything-but-true = normal entity (the default).
+// Set via `gbrain reference <slug>` (or hand-edit frontmatter).
+
+export const REFERENCE_FRONTMATTER_KEY = 'reference';
+
+/**
+ * SQL predicate (true for NON-reference pages) to AND into entity-coverage
+ * denominators AND numerators so the ratio stays consistent. JSONB `->>` yields
+ * text; `IS DISTINCT FROM 'true'` treats absent (NULL) and every non-true value
+ * as a normal counted entity. Backed by the GIN index on `pages.frontmatter`.
+ *
+ * @param alias optional table alias (e.g. 'p' for `pages p`); omit for bare `pages`.
+ *
+ * NOTE: postgres-engine.ts uses a postgres.js tagged template where `${}` is a
+ * bound parameter, not raw SQL, so it inlines this predicate literally — keep
+ * the two in sync.
+ */
+export function referenceExclusionSql(alias = ''): string {
+  const col = alias ? `${alias}.frontmatter` : 'frontmatter';
+  return `(${col}->>'${REFERENCE_FRONTMATTER_KEY}') IS DISTINCT FROM 'true'`;
+}

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/reference-flag.test.ts

@@ -0,0 +1,154 @@
+import { describe, expect, test } from 'bun:test';
+import { referenceExclusionSql, REFERENCE_FRONTMATTER_KEY } from '../src/core/reference-flag.ts';
+import { applyReferenceFrontmatter } from '../src/commands/reference.ts';
+
+describe('referenceExclusionSql', () => {
+  test('bare pages (no alias)', () => {
+    expect(referenceExclusionSql()).toBe(`(frontmatter->>'reference') IS DISTINCT FROM 'true'`);
+  });
+  test('aliased', () => {
+    expect(referenceExclusionSql('p')).toBe(`(p.frontmatter->>'reference') IS DISTINCT FROM 'true'`);
+  });
+  test('key constant', () => {
+    expect(REFERENCE_FRONTMATTER_KEY).toBe('reference');
+  });
+});
+
+describe('applyReferenceFrontmatter', () => {
+  const page = `---\ntitle: Andy Grove\ntype: person\ntags: []\n---\n\n# Andy Grove\n\nBody.`;
+
+  test('adds reference: true to an existing frontmatter block', () => {
+    const out = applyReferenceFrontmatter(page, true);
+    expect(out).toContain('reference: true');
+    expect(out).toContain('type: person');   // other keys preserved
+    expect(out).toContain('# Andy Grove');    // body preserved
+  });
+
+  test('is idempotent — does not duplicate the key', () => {
+    const once = applyReferenceFrontmatter(page, true);
+    const twice = applyReferenceFrontmatter(once, true);
+    expect(twice).toBe(once);
+    expect(twice.match(/reference: true/g)).toHaveLength(1);
+  });
+
+  test('replaces a stale reference: false with true', () => {
+    const off = `---\ntype: person\nreference: false\n---\n\nBody.`;
+    const out = applyReferenceFrontmatter(off, true);
+    expect(out).toContain('reference: true');
+    expect(out).not.toContain('reference: false');
+  });
+
+  test('--unset removes the key', () => {
+    const on = applyReferenceFrontmatter(page, true);
+    const off = applyReferenceFrontmatter(on, false);
+    expect(off).not.toContain('reference:');
+    expect(off).toContain('type: person');
+  });
+
+  test('--unset on a page without the key is a no-op', () => {
+    expect(applyReferenceFrontmatter(page, false)).toBe(page);
+  });
+
+  test('setting on a frontmatter-less page prepends a block', () => {
+    const raw = '# Just a heading\n\nNo frontmatter here.';
+    const out = applyReferenceFrontmatter(raw, true);
+    expect(out.startsWith('---\nreference: true\n---\n')).toBe(true);
+    expect(out).toContain('# Just a heading');
+  });
+
+  test('preserves body containing YAML-special chars', () => {
+    const tricky = `---\ntype: person\n---\n\nText with $& and $1 literals.`;
+    const out = applyReferenceFrontmatter(tricky, true);
+    expect(out).toContain('Text with $& and $1 literals.');
+    expect(out).toContain('reference: true');
+  });
+});
+
+// ── e2e: getHealth exemption + (source_id, slug)-scoped JSONB write ─────────
+
+import { afterAll, beforeAll } from 'bun:test';
+import * as fs from 'node:fs';
+import * as os from 'node:os';
+import * as path from 'node:path';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { runReference } from '../src/commands/reference.ts';
+import { withEnv } from './helpers/with-env.ts';
+
+describe('reference flag e2e (PGLite)', () => {
+  let engine: PGLiteEngine;
+  let brainDir: string;
+
+  beforeAll(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({ database_url: '' });
+    await engine.initSchema();
+
+    brainDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gbrain-ref-'));
+    fs.mkdirSync(path.join(brainDir, 'people'), { recursive: true });
+    fs.writeFileSync(
+      path.join(brainDir, 'people/andy-grove.md'),
+      '---\ntitle: Andy Grove\ntype: person\n---\n\n# Andy Grove\n',
+      'utf8',
+    );
+
+    await engine.executeRaw(
+      `INSERT INTO sources (id, name, local_path, config, created_at)
+       VALUES ('src-a', 'a', $1, '{}'::jsonb, now()), ('src-b', 'b', NULL, '{}'::jsonb, now())`,
+      [brainDir],
+    );
+    // Same slug in BOTH sources — the write must only touch src-a.
+    await engine.putPage('people/andy-grove', {
+      type: 'person', title: 'Andy Grove', compiled_truth: 'canon figure',
+    }, { sourceId: 'src-a' });
+    await engine.putPage('people/andy-grove', {
+      type: 'person', title: 'Andy Grove', compiled_truth: 'other-source twin',
+    }, { sourceId: 'src-b' });
+    // A normal contact WITH a timeline entry, so coverage has a live numerator.
+    const contact = await engine.putPage('people/alice-example', {
+      type: 'person', title: 'Alice Example', compiled_truth: 'real contact',
+    }, { sourceId: 'src-a' });
+    await engine.executeRaw(
+      `INSERT INTO timeline_entries (page_id, date, summary) VALUES ($1, '2026-01-01', 'met')`,
+      [contact.id],
+    );
+  });
+
+  afterAll(async () => {
+    await engine.disconnect();
+    fs.rmSync(brainDir, { recursive: true, force: true });
+  });
+
+  test('runReference scopes the JSONB write to the resolved (source_id, slug)', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () =>
+      runReference(engine, ['people/andy-grove', '--brain', brainDir]));
+
+    const rows = await engine.executeRaw<{ source_id: string; ref: string | null }>(
+      `SELECT source_id, frontmatter->>'reference' AS ref FROM pages WHERE slug = 'people/andy-grove' ORDER BY source_id`,
+    );
+    expect(rows).toEqual([
+      { source_id: 'src-a', ref: 'true' },
+      { source_id: 'src-b', ref: null },   // twin in the other source untouched
+    ]);
+    // Durable half: frontmatter on disk got the flag too.
+    expect(fs.readFileSync(path.join(brainDir, 'people/andy-grove.md'), 'utf8'))
+      .toContain('reference: true');
+  });
+
+  test('getHealth exempts reference pages from timeline/link coverage', async () => {
+    const health = await engine.getHealth();
+    // 3 person pages; the 2 reference-less twins would drag coverage to 1/3.
+    // With the src-a twin marked reference, denominator = 2 (alice + src-b twin).
+    expect(health.timeline_coverage).toBeCloseTo(0.5);
+  });
+
+  test('unset restores the page to a normal counted entity', async () => {
+    await withEnv({ GBRAIN_SOURCE: undefined }, () =>
+      runReference(engine, ['people/andy-grove', '--unset', '--brain', brainDir]));
+    const rows = await engine.executeRaw<{ ref: string | null }>(
+      `SELECT frontmatter->>'reference' AS ref FROM pages WHERE slug = 'people/andy-grove' AND source_id = 'src-a'`,
+    );
+    expect(rows[0].ref).toBeNull();
+    const health = await engine.getHealth();
+    expect(health.timeline_coverage).toBeCloseTo(1 / 3);
+  });
+});