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>

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/models.ts

@@ -50,10 +50,6 @@ const PER_TASK_KEYS: Array<{ key: string; tier: ModelTier; description: string }
   { key: 'models.eval.contradictions_judge', tier: 'utility',  description: 'Contradiction probe judge (v0.34 temporal-aware)' },
   { key: 'models.expansion',                tier: 'utility',   description: 'Query expansion for hybrid search' },
   { key: 'models.chat',                     tier: 'reasoning', description: 'Default `gateway.chat()` model' },
-  { key: 'models.propose_takes',            tier: 'reasoning', description: 'propose_takes claim extractor' },
-  { key: 'models.grade_takes',              tier: 'reasoning', description: 'grade_takes verdict judge' },
-  { key: 'models.calibration_profile',      tier: 'reasoning', description: 'Calibration profile generator' },
-  { key: 'models.brainstorm',               tier: 'reasoning', description: '`gbrain brainstorm` orchestrator' },
 ];
 
 interface ModelEntry {

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/core/brainstorm/judges.ts

@@ -61,10 +61,7 @@ export const MAX_OUTPUT_TOKENS_CEIL = 32_000;
  * (with a readable error) instead of the provider's opaque HTTP 400.
  */
 export const ANTHROPIC_OUTPUT_CAPS: Record<string, number> = {
-  'claude-fable-5': 64_000,
-  'claude-opus-4-8': 32_000,
   'claude-opus-4-7': 32_000,
-  'claude-sonnet-5': 64_000,
   'claude-sonnet-4-6': 64_000,
   'claude-haiku-4-5': 64_000,
   'claude-haiku-4-5-20251001': 64_000,

src/core/brainstorm/orchestrator.ts

@@ -32,7 +32,6 @@
  */
 
 import type { BrainEngine } from '../engine.ts';
-import { resolveModel } from '../model-config.ts';
 import { chat as defaultChat, embedQuery, type ChatResult, type ChatOpts } from '../ai/gateway.ts';
 import { hybridSearch, hybridSearchCached } from '../search/hybrid.ts';
 import { fetchFar, type CloseRef, type FarPage } from './domain-bank.ts';
@@ -539,14 +538,7 @@ async function _runBrainstormInner(
   const embedFn = opts.embedQueryFn ?? embedQuery;
 
   // ---- Phase 0: cost preview + TTY grace ----
-  // Tier-resolved (mirrors the cycle phases): honors models.brainstorm >
-  // models.default > models.tier.reasoning; the fallback keeps stock
-  // behavior identical (reasoning tier default IS claude-sonnet-4-6).
-  const modelStr = opts.modelOverride ?? await resolveModel(engine, {
-    configKey: 'models.brainstorm',
-    tier: 'reasoning',
-    fallback: 'anthropic:claude-sonnet-4-6',
-  });
+  const modelStr = opts.modelOverride ?? 'anthropic:claude-sonnet-4-6';
   const { aborted, estimate } = await previewCostAndWait({
     profile,
     model: modelStr,

src/core/cycle/calibration-profile.ts

@@ -26,8 +26,8 @@
  */
 
 import { BaseCyclePhase, type ScopedReadOpts, type BasePhaseOpts } from './base-phase.ts';
-import { chat as gatewayChat, getChatModel } from '../ai/gateway.ts';
-import { resolveModel } from '../model-config.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';
 import { patternStatementTemplate, type PatternStatementSlots } from '../calibration/templates.ts';
 // v0.41 T10 — domain widening. The aggregator module resolves the active
@@ -229,16 +229,7 @@ class CalibrationProfilePhase extends BaseCyclePhase {
   ): Promise<{ summary: string; details: Record<string, unknown>; status?: PhaseStatus }> {
     const holder = opts.holder ?? 'garry';
     const promptVersion = opts.promptVersion ?? CALIBRATION_PROFILE_PROMPT_VERSION;
-    // Resolved once (see propose-takes.ts for the chain): models.calibration_profile
-    // > models.default > env > the gateway's chat model (itself resolved
-    // through models.chat + the reasoning tier). Provider-prefixed per #2451
-    // — a bare id would make gateway.chat() throw "missing a provider
-    // prefix". Drives the generator's chat call, the budget label, and the
-    // persisted model_id, so the three can never disagree.
-    const modelId = opts.model ?? await resolveModel(engine, {
-      configKey: 'models.calibration_profile',
-      fallback: getChatModel(),
-    });
+    const modelId = opts.model ?? TIER_DEFAULTS.reasoning;
     const gradeCompletion = opts.gradeCompletion ?? 1.0;
     const patternsGenerator = opts.patternsGenerator ?? defaultPatternsGenerator;
     const biasTagsGenerator = opts.biasTagsGenerator ?? defaultBiasTagsGenerator;
@@ -274,7 +265,6 @@ class CalibrationProfilePhase extends BaseCyclePhase {
         scorecard,
         holder,
         attempt,
-        modelHint: modelId,
         ...(feedback !== undefined ? { feedback } : {}),
       });
       return lines.join('\n');

src/core/cycle/grade-takes.ts

@@ -36,9 +36,7 @@
 
 import { createHash } from 'node:crypto';
 import { BaseCyclePhase, type ScopedReadOpts, type BasePhaseOpts } from './base-phase.ts';
-import { chat as gatewayChat, getChatModel } from '../ai/gateway.ts';
-import { resolveModel } from '../model-config.ts';
-import { splitProviderModelId } from '../model-id.ts';
+import { chat as gatewayChat } from '../ai/gateway.ts';
 import { GBrainError } from '../types.ts';
 import type { OperationContext } from '../operations.ts';
 import type { BrainEngine, Take, TakeResolution } from '../engine.ts';
@@ -397,24 +395,7 @@ class GradeTakesPhase extends BaseCyclePhase {
     const autoResolve = opts.autoResolve ?? false; // D17 default OFF
     const autoResolveThreshold = opts.autoResolveThreshold ?? 0.95; // D12 conservative
     const resolvedByLabel = opts.resolvedByLabel ?? 'gbrain:grade_takes';
-    // Resolve the judge model ONCE (see propose-takes.ts for the chain —
-    // same label-vs-actual split fixed here: the judge call rode the
-    // gateway's chat_model while the grade cache key, evidence signature,
-    // and budget label recorded a hardcoded 4.6).
-    // NOTE: changing the resolved judge model invalidates the grade cache
-    // (judge_model_id is part of its key) — a one-time, budget-capped
-    // re-grade wave that is CORRECT, since the actual judge did change.
-    const judgeModelFull = opts.model ?? await resolveModel(engine, {
-      configKey: 'models.grade_takes',
-      fallback: getChatModel(),
-    });
-    // Bare tail for cache keys / evidence signatures / stored ids — the
-    // grade cache has always been keyed on bare ids; the gateway default
-    // resolves provider-prefixed, and normalizing preserves cache continuity
-    // on stock installs (no spurious re-judge wave from a prefix change). A
-    // genuinely different configured judge still invalidates, which is
-    // correct. The FULL string drives the actual judge call.
-    const judgeModelId = splitProviderModelId(judgeModelFull).model || judgeModelFull;
+    const judgeModelId = opts.model ?? 'claude-sonnet-4-6';
 
     const useEnsemble = opts.useEnsemble ?? false;
     const ensembleThreshold = opts.ensembleThreshold ?? 0.85;
@@ -487,7 +468,7 @@ class GradeTakesPhase extends BaseCyclePhase {
       // Call the single-model judge. Errors on a single take log warning + continue.
       let verdict: JudgeVerdict;
       try {
-        verdict = await judge({ take, evidence, modelHint: judgeModelFull });
+        verdict = await judge({ take, evidence, modelHint: opts.model });
       } catch (err) {
         const msg = err instanceof Error ? err.message : String(err);
         result.warnings.push(`judge failed on take ${take.id}: ${msg}`);

src/core/cycle/propose-takes.ts

@@ -5,16 +5,11 @@
  * a tuned LLM extractor, writes the extracted gradeable claims to the
  * `take_proposals` queue. User accepts/rejects via `gbrain takes propose`.
  *
- * Idempotency contract (D17 schema spec; per-claim rows since migration v125):
- *   Every scan of a (source_id, page_slug, content_hash, prompt_version)
- *   tuple leaves at least one row — one per extracted claim, or a single
- *   status='empty' sentinel when extraction yields nothing — so an unchanged
- *   page never re-spends LLM tokens. Pre-v125 only proposal rows were
- *   written: a zero-claim page never entered the cache and was re-extracted
- *   on EVERY cycle (observed live: ~60 such pages × every cycle ≈ 1,400
- *   wasted extractor calls / ~$15 per day — ~90% of total autopilot spend).
- *   Bumping PROPOSE_TAKES_PROMPT_VERSION cleanly invalidates the cache so a
- *   tuned prompt re-runs proposals on every page.
+ * Idempotency contract (D17 schema spec):
+ *   The unique index on (source_id, page_slug, content_hash, prompt_version)
+ *   means an unchanged page never re-spends LLM tokens. Bumping
+ *   PROPOSE_TAKES_PROMPT_VERSION cleanly invalidates the cache so a tuned
+ *   prompt re-runs proposals on every page.
  *
  * F2 fence dedup:
  *   The phase reads the page's existing `<!-- gbrain:takes:begin -->` fence
@@ -45,7 +40,6 @@
 import { randomUUID, createHash } from 'node:crypto';
 import { BaseCyclePhase, type ScopedReadOpts, type BasePhaseOpts } from './base-phase.ts';
 import { chat as gatewayChat, getChatModel } from '../ai/gateway.ts';
-import { resolveModel } from '../model-config.ts';
 import { writeReceipt } from '../extract/receipt-writer.ts';
 import { upsertExtractRollup } from '../extract/rollup-writer.ts';
 import { GBrainError } from '../types.ts';
@@ -313,18 +307,6 @@ class ProposeTakesPhase extends BaseCyclePhase {
     const promptVersion = opts.promptVersion ?? PROPOSE_TAKES_PROMPT_VERSION;
     const pageLimit = opts.pageLimit ?? 100;
     const skipPagesWithFence = opts.skipPagesWithFence ?? false;
-    // Resolve the extractor model ONCE: models.propose_takes >
-    // models.default > GBRAIN_MODEL env > the gateway's chat model (which
-    // reconfigureGatewayWithEngine already resolved through models.chat +
-    // the reasoning tier). One resolved provider-prefixed string drives the
-    // actual chat call, the budget estimate, AND the stored model_id — so
-    // the recorded model can never disagree with the model that ran (#2451
-    // convention: stored ids are provider-prefixed, nested prefixes like
-    // openrouter:anthropic/... stay intact).
-    const extractorModelId = opts.model ?? await resolveModel(engine, {
-      configKey: 'models.propose_takes',
-      fallback: getChatModel(),
-    });
     const proposalRunId = `propose-${new Date().toISOString().slice(0, 19).replace(/[-:T]/g, '')}-${randomUUID().slice(0, 8)}`;
 
     const result: ProposeTakesResult = {
@@ -348,6 +330,8 @@ class ProposeTakesPhase extends BaseCyclePhase {
       opts.reporter.start('propose_takes.pages' as never, pages.length);
     }
 
+    const modelId = opts.model ?? getChatModel();
+
     for (const page of pages) {
       result.pages_scanned += 1;
       this.tick(opts);
@@ -377,7 +361,7 @@ class ProposeTakesPhase extends BaseCyclePhase {
 
       // Budget pre-check before the LLM call. Estimate: ~1500 input tokens + 500 output.
       const budget = this.checkBudget({
-        modelId: extractorModelId,
+        modelId,
         estimatedInputTokens: 1500,
         maxOutputTokens: 500,
       });
@@ -396,7 +380,7 @@ class ProposeTakesPhase extends BaseCyclePhase {
           pagePath: page.slug,
           pageBody: body,
           existingTakes,
-          modelHint: extractorModelId,
+          modelHint: opts.model,
         });
       } catch (err) {
         const msg = err instanceof Error ? err.message : String(err);
@@ -404,42 +388,16 @@ class ProposeTakesPhase extends BaseCyclePhase {
         continue;
       }
 
-      // Zero-claim scans MUST still enter the idempotency cache. Pre-v125
-      // only proposal rows were written, so a page whose extraction yielded
-      // no gradeable claims never got a row for its (page, content_hash) —
-      // the cache check above missed on every subsequent cycle and the LLM
-      // call was re-spent on the same unchanged page, forever. The sentinel
-      // row (status='empty', empty claim_text) is invisible to the review
-      // queue (pending_idx is partial on status='pending'); it exists only
-      // so the cache check hits.
-      if (proposals.length === 0) {
-        await engine.executeRaw(
-          `INSERT INTO take_proposals
-             (source_id, page_slug, content_hash, prompt_version, proposal_run_id,
-              status, claim_text, kind, holder, weight, domain, dedup_against_fence_rows, model_id)
-           VALUES ($1, $2, $3, $4, $5, 'empty', '', 'none', 'brain', 0, NULL, NULL, $6)
-           ON CONFLICT (source_id, page_slug, content_hash, prompt_version, md5(claim_text)) DO NOTHING`,
-          [sourceId, page.slug, ch, promptVersion, proposalRunId, extractorModelId],
-        );
-        continue;
-      }
-
-      // Write proposals to take_proposals, one row per claim. The v125
-      // idempotency index includes md5(claim_text), so a same-page
-      // multi-claim run keeps EVERY claim — the pre-v125 four-column unique
-      // index made claims 2..N conflict with claim 1 and ON CONFLICT DO
-      // NOTHING silently dropped them (the review queue only ever saw the
-      // first claim of each page version). RETURNING id keeps
-      // proposals_inserted honest: it counts rows that actually landed,
-      // not insert attempts.
+      // Write proposals to take_proposals. Each row is a separate INSERT
+      // because the composite idempotency key is on the per-page tuple — a
+      // bulk UPSERT would collapse a same-page-multi-claim run into one row.
       for (const p of proposals) {
-        const landed = await engine.executeRaw<{ id: number }>(
+        await engine.executeRaw(
           `INSERT INTO take_proposals
              (source_id, page_slug, content_hash, prompt_version, proposal_run_id,
               claim_text, kind, holder, weight, domain, dedup_against_fence_rows, model_id)
            VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12)
-           ON CONFLICT (source_id, page_slug, content_hash, prompt_version, md5(claim_text)) DO NOTHING
-           RETURNING id`,
+           ON CONFLICT (source_id, page_slug, content_hash, prompt_version) DO NOTHING`,
           [
             sourceId,
             page.slug,
@@ -452,10 +410,10 @@ class ProposeTakesPhase extends BaseCyclePhase {
             p.weight,
             p.domain ?? null,
             JSON.stringify(existingTakes),
-            extractorModelId,
+            modelId,
           ],
         );
-        if (landed.length > 0) result.proposals_inserted += 1;
+        result.proposals_inserted += 1;
       }
     }
 

src/core/cycle/synthesize.ts

@@ -58,11 +58,8 @@ const SUMMARY_SLUG_RE = /^[a-z0-9][a-z0-9\-]*(\/[a-z0-9][a-z0-9\-]*)*$/;
  * resolver returns for known Anthropic aliases.
  */
 const MODEL_CONTEXT_TOKENS: Record<string, number> = {
-  'claude-fable-5': 1_000_000,
-  'claude-opus-4-8': 1_000_000,
   'claude-opus-4-7': 1_000_000,
   'claude-opus-4-6': 1_000_000,
-  'claude-sonnet-5': 1_000_000,
   'claude-sonnet-4-6': 200_000,
   'claude-sonnet-4-5': 200_000,
   'claude-haiku-4-5-20251001': 200_000,

src/core/migrate.ts

@@ -5671,41 +5671,6 @@ export const MIGRATIONS: Migration[] = [
 `);
     },
   },
-  {
-    version: 125,
-    name: 'take_proposals_empty_scan_sentinels_and_per_claim_rows',
-    // v0.42.x — kill the propose_takes rescan loop + stop dropping claims.
-    //
-    // Two defects, one schema touch:
-    //   1. Zero-claim scans never entered the idempotency cache (only
-    //      proposal rows were written), so pages whose extraction yielded
-    //      nothing were re-extracted on EVERY cycle. Observed live: ~60
-    //      such pages per run ≈ 1,400 wasted extractor calls / ~$15 per
-    //      day — ~90% of total autopilot LLM spend. Fix: the phase now
-    //      writes a status='empty' sentinel row per zero-claim scan; the
-    //      status CHECK gains the 'empty' value. Sentinels are excluded
-    //      from the partial pending index, so the review queue never sees
-    //      them.
-    //   2. The 4-column unique index collapsed a same-page multi-claim run
-    //      to its FIRST claim: rows 2..N conflicted and ON CONFLICT DO
-    //      NOTHING silently dropped them (verified live: exactly one row
-    //      per (page, hash) across 3 days of runs). Fix: the idempotency
-    //      index gains md5(claim_text) — per-claim rows, while the
-    //      4-column prefix still serves the per-scan cache lookup.
-    //
-    // Existing data is index-safe by construction: the old index guaranteed
-    // at most one row per 4-tuple, so the widened index has no duplicates
-    // to trip on. The DROP+ADD CONSTRAINT pair is idempotent as a unit.
-    idempotent: true,
-    sql: `
-      ALTER TABLE take_proposals DROP CONSTRAINT IF EXISTS take_proposals_status_check;
-      ALTER TABLE take_proposals ADD CONSTRAINT take_proposals_status_check
-        CHECK (status IN ('pending','accepted','rejected','superseded','empty'));
-      DROP INDEX IF EXISTS take_proposals_idempotency_idx;
-      CREATE UNIQUE INDEX IF NOT EXISTS take_proposals_idempotency_idx
-        ON take_proposals (source_id, page_slug, content_hash, prompt_version, md5(claim_text));
-    `,
-  },
 ];
 
 export const LATEST_VERSION = MIGRATIONS.length > 0

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/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/pglite-schema.ts

@@ -762,7 +762,7 @@ CREATE TABLE IF NOT EXISTS take_proposals (
   proposed_at                 TIMESTAMPTZ  NOT NULL DEFAULT now(),
   proposal_run_id             TEXT         NOT NULL,
   status                      TEXT         NOT NULL DEFAULT 'pending'
-                                           CHECK (status IN ('pending','accepted','rejected','superseded','empty')),
+                                           CHECK (status IN ('pending','accepted','rejected','superseded')),
   claim_text                  TEXT         NOT NULL,
   kind                        TEXT         NOT NULL,
   holder                      TEXT         NOT NULL,
@@ -777,7 +777,7 @@ CREATE TABLE IF NOT EXISTS take_proposals (
   predicted_brier_bucket_n    INTEGER
 );
 CREATE UNIQUE INDEX IF NOT EXISTS take_proposals_idempotency_idx
-  ON take_proposals (source_id, page_slug, content_hash, prompt_version, md5(claim_text));
+  ON take_proposals (source_id, page_slug, content_hash, prompt_version);
 CREATE INDEX IF NOT EXISTS take_proposals_pending_idx
   ON take_proposals (source_id, status, proposed_at DESC)
   WHERE status = 'pending';

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/schema-embedded.ts

@@ -1274,14 +1274,8 @@ CREATE INDEX IF NOT EXISTS calibration_profiles_published_idx
   WHERE published = true;
 
 -- take_proposals: propose_takes phase queue. Idempotency cache via the
--- composite unique index (source_id, page_slug, content_hash, prompt_version,
--- md5(claim_text)) — the 4-column prefix is the per-scan cache key (mirrors
--- v0.23 dream_verdicts); md5(claim_text) makes rows per-claim so multi-claim
--- pages keep every claim (v125). status='empty' rows are zero-claim scan
--- sentinels: they hold the cache slot for a page version whose extraction
--- yielded nothing — the phase never re-spends the LLM call on that page
--- version. Excluded from the partial pending index. proposal_run_id supports
--- --rollback by run.
+-- composite unique index (source_id, page_slug, content_hash, prompt_version)
+-- mirrors v0.23 dream_verdicts. proposal_run_id supports --rollback by run.
 CREATE TABLE IF NOT EXISTS take_proposals (
   id                          BIGSERIAL PRIMARY KEY,
   source_id                   TEXT         NOT NULL REFERENCES sources(id) ON DELETE CASCADE,
@@ -1292,7 +1286,7 @@ CREATE TABLE IF NOT EXISTS take_proposals (
   proposed_at                 TIMESTAMPTZ  NOT NULL DEFAULT now(),
   proposal_run_id             TEXT         NOT NULL,
   status                      TEXT         NOT NULL DEFAULT 'pending'
-                                           CHECK (status IN ('pending','accepted','rejected','superseded','empty')),
+                                           CHECK (status IN ('pending','accepted','rejected','superseded')),
   claim_text                  TEXT         NOT NULL,
   kind                        TEXT         NOT NULL,
   holder                      TEXT         NOT NULL,
@@ -1307,7 +1301,7 @@ CREATE TABLE IF NOT EXISTS take_proposals (
   predicted_brier_bucket_n    INTEGER
 );
 CREATE UNIQUE INDEX IF NOT EXISTS take_proposals_idempotency_idx
-  ON take_proposals (source_id, page_slug, content_hash, prompt_version, md5(claim_text));
+  ON take_proposals (source_id, page_slug, content_hash, prompt_version);
 CREATE INDEX IF NOT EXISTS take_proposals_pending_idx
   ON take_proposals (source_id, status, proposed_at DESC)
   WHERE status = 'pending';

src/schema.sql

@@ -1270,14 +1270,8 @@ CREATE INDEX IF NOT EXISTS calibration_profiles_published_idx
   WHERE published = true;
 
 -- take_proposals: propose_takes phase queue. Idempotency cache via the
--- composite unique index (source_id, page_slug, content_hash, prompt_version,
--- md5(claim_text)) — the 4-column prefix is the per-scan cache key (mirrors
--- v0.23 dream_verdicts); md5(claim_text) makes rows per-claim so multi-claim
--- pages keep every claim (v125). status='empty' rows are zero-claim scan
--- sentinels: they hold the cache slot for a page version whose extraction
--- yielded nothing — the phase never re-spends the LLM call on that page
--- version. Excluded from the partial pending index. proposal_run_id supports
--- --rollback by run.
+-- composite unique index (source_id, page_slug, content_hash, prompt_version)
+-- mirrors v0.23 dream_verdicts. proposal_run_id supports --rollback by run.
 CREATE TABLE IF NOT EXISTS take_proposals (
   id                          BIGSERIAL PRIMARY KEY,
   source_id                   TEXT         NOT NULL REFERENCES sources(id) ON DELETE CASCADE,
@@ -1288,7 +1282,7 @@ CREATE TABLE IF NOT EXISTS take_proposals (
   proposed_at                 TIMESTAMPTZ  NOT NULL DEFAULT now(),
   proposal_run_id             TEXT         NOT NULL,
   status                      TEXT         NOT NULL DEFAULT 'pending'
-                                           CHECK (status IN ('pending','accepted','rejected','superseded','empty')),
+                                           CHECK (status IN ('pending','accepted','rejected','superseded')),
   claim_text                  TEXT         NOT NULL,
   kind                        TEXT         NOT NULL,
   holder                      TEXT         NOT NULL,
@@ -1303,7 +1297,7 @@ CREATE TABLE IF NOT EXISTS take_proposals (
   predicted_brier_bucket_n    INTEGER
 );
 CREATE UNIQUE INDEX IF NOT EXISTS take_proposals_idempotency_idx
-  ON take_proposals (source_id, page_slug, content_hash, prompt_version, md5(claim_text));
+  ON take_proposals (source_id, page_slug, content_hash, prompt_version);
 CREATE INDEX IF NOT EXISTS take_proposals_pending_idx
   ON take_proposals (source_id, status, proposed_at DESC)
   WHERE status = 'pending';

test/calibration-profile.test.ts

@@ -38,7 +38,6 @@ function buildMockEngine(opts: { scorecard: TakesScorecard }): {
 } {
   const captured: CapturedSql[] = [];
   const engine = {
-    async getConfig() { return null; },
     kind: 'pglite',
     async getScorecard() {
       return opts.scorecard;

test/grade-takes-ensemble.test.ts

@@ -47,7 +47,6 @@ function buildMockEngine(opts: { takes: Take[] }): {
   const captured: CapturedSql[] = [];
   const resolves: CapturedResolve[] = [];
   const engine = {
-    async getConfig() { return null; },
     kind: 'pglite',
     async listTakes() {
       return opts.takes;

test/grade-takes.test.ts

@@ -46,14 +46,12 @@ interface CapturedResolve {
 function buildMockEngine(opts: {
   takes: Take[];
   cachedGrades?: Set<string>; // composite-key strings already in take_grade_cache
-  config?: Record<string, string>; // engine.getConfig plane (models.grade_takes etc.)
 }): { engine: BrainEngine; captured: CapturedSql[]; resolves: CapturedResolve[] } {
   const captured: CapturedSql[] = [];
   const resolves: CapturedResolve[] = [];
   const cached = opts.cachedGrades ?? new Set<string>();
 
   const engine = {
-    async getConfig(key: string) { return opts.config?.[key] ?? null; },
     kind: 'pglite',
     async listTakes() {
       return opts.takes;
@@ -226,28 +224,6 @@ describe('runPhaseGradeTakes — phase integration', () => {
     expect(resolves).toHaveLength(0); // no canonical mutation
   });
 
-  test('models.grade_takes config drives the judge call; cache key stays bare-tailed', async () => {
-    // Pre-fix the judge call rode the gateway's chat_model while the cache
-    // key / budget label recorded a hardcoded 'claude-sonnet-4-6'. The phase
-    // now resolves models.grade_takes; the judge gets the FULL string and
-    // the cache row keys on the bare tail (continuity with historical rows).
-    const takes = [buildTake({ id: 1, sinceDate: '2023-01-01' })];
-    const { engine, captured } = buildMockEngine({
-      takes,
-      config: { 'models.grade_takes': 'anthropic:claude-sonnet-5' },
-    });
-    const hints: Array<string | undefined> = [];
-    const judge: JudgeFn = async ({ modelHint }) => {
-      hints.push(modelHint);
-      return { verdict: 'correct', confidence: 0.9, reasoning: 'held' };
-    };
-    const result = await runPhaseGradeTakes(buildCtx(engine), { judge });
-    expect(result.status).toBe('ok');
-    expect(hints).toEqual(['anthropic:claude-sonnet-5']); // actual call gets the FULL string
-    const inserts = captured.filter(c => c.sql.includes('INSERT INTO take_grade_cache'));
-    expect(inserts[0]!.params[2]).toBe('claude-sonnet-5'); // judge_model_id is the bare tail
-  });
-
   test('D17: auto-resolve OFF by default — even high-confidence verdict does NOT mutate takes', async () => {
     const takes = [buildTake({ id: 1, sinceDate: '2023-01-01' })];
     const { engine, resolves } = buildMockEngine({ takes });

test/propose-takes-rescan.test.ts

@@ -1,160 +0,0 @@
-/**
- * propose_takes rescan-loop + dropped-claims regression tests (migration v125).
- *
- * Two live-observed defects, both fixed by the v125 schema + phase change:
- *
- *   1. RESCAN LOOP — a page whose extraction yielded zero claims never
- *      entered the idempotency cache (only proposal rows were written), so
- *      every cycle re-spent the extractor call on the same unchanged page.
- *      Live impact: ~60 such pages × every cycle ≈ 1,400 wasted LLM calls
- *      (~$15) per day — ~90% of total autopilot spend. Fix: status='empty'
- *      sentinel row per zero-claim scan.
- *
- *   2. DROPPED CLAIMS — the 4-column unique index collapsed a same-page
- *      multi-claim run to its first claim (rows 2..N conflicted, ON CONFLICT
- *      DO NOTHING dropped them silently; verified live: exactly 1 row per
- *      (page, hash) over 3 days). Fix: idempotency index gains
- *      md5(claim_text).
- *
- * Hermetic: PGLite engine + injected extractor; no gateway, no LLM.
- */
-import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
-import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { runPhaseProposeTakes, type ProposeTakesExtractor, type ProposedTake } from '../src/core/cycle/propose-takes.ts';
-import type { OperationContext } from '../src/core/operations.ts';
-
-let engine: PGLiteEngine;
-
-function ctx(): OperationContext {
-  return {
-    engine,
-    remote: false,
-    config: {} as OperationContext['config'],
-    logger: { info() {}, warn() {}, error() {}, debug() {} } as unknown as OperationContext['logger'],
-  } as unknown as OperationContext;
-}
-
-/** Extractor stub that counts invocations per page slug. */
-function countingExtractor(
-  claimsBySlug: Record<string, ProposedTake[]>,
-): { extractor: ProposeTakesExtractor; calls: string[] } {
-  const calls: string[] = [];
-  const extractor: ProposeTakesExtractor = async ({ pagePath }) => {
-    calls.push(pagePath);
-    return claimsBySlug[pagePath] ?? [];
-  };
-  return { extractor, calls };
-}
-
-beforeAll(async () => {
-  engine = new PGLiteEngine();
-  await engine.connect({});
-  await engine.initSchema();
-  await engine.putPage('notes/zero-claims', {
-    type: 'note',
-    title: 'pure narrative',
-    compiled_truth: 'A quiet walk in the park. Nothing opinionated happened at all today.',
-  });
-  await engine.putPage('notes/three-claims', {
-    type: 'note',
-    title: 'opinionated',
-    compiled_truth: 'I bet acme-example wins the market. widget-co will struggle. fund-a is overexposed.',
-  });
-});
-
-afterAll(async () => {
-  await engine.disconnect();
-});
-
-describe('rescan loop — zero-claim scans enter the cache', () => {
-  test('second run cache-hits: extractor is NOT called again on unchanged pages', async () => {
-    const claims = {
-      'notes/three-claims': [
-        { claim_text: 'acme-example wins the market', kind: 'bet' as const, holder: 'brain', weight: 0.7 },
-        { claim_text: 'widget-co will struggle', kind: 'take' as const, holder: 'brain', weight: 0.6 },
-        { claim_text: 'fund-a is overexposed', kind: 'take' as const, holder: 'brain', weight: 0.55 },
-      ],
-    };
-
-    const first = countingExtractor(claims);
-    const r1 = await runPhaseProposeTakes(ctx(), { extractor: first.extractor });
-    expect(r1.status).toBe('ok');
-    // Both pages extracted on the first pass.
-    expect(first.calls).toContain('notes/zero-claims');
-    expect(first.calls).toContain('notes/three-claims');
-
-    const second = countingExtractor(claims);
-    const r2 = await runPhaseProposeTakes(ctx(), { extractor: second.extractor });
-    expect(r2.status).toBe('ok');
-    // THE regression: pre-fix the zero-claim page missed the cache every
-    // run and was re-extracted here. (Run 1's receipt page legitimately
-    // appears once — it's a new page — and its zero-claim scan now caches
-    // too; pre-fix, receipts re-scanned forever as well.)
-    expect(second.calls).not.toContain('notes/zero-claims');
-    expect(second.calls).not.toContain('notes/three-claims');
-
-    // Run 2 inserted nothing, so no new receipt page exists: run 3 must be
-    // fully quiescent — zero extractor calls, zero cache misses.
-    const third = countingExtractor(claims);
-    const r3 = await runPhaseProposeTakes(ctx(), { extractor: third.extractor });
-    expect(r3.status).toBe('ok');
-    expect(third.calls).toEqual([]);
-    expect((r3.details as Record<string, unknown>).cache_misses).toBe(0);
-  });
-
-  test('zero-claim scan wrote an "empty" sentinel invisible to the pending queue', async () => {
-    const sentinel = await engine.executeRaw<{ status: string; claim_text: string }>(
-      `SELECT status, claim_text FROM take_proposals WHERE page_slug = 'notes/zero-claims'`,
-      [],
-    );
-    expect(sentinel.length).toBe(1);
-    expect(sentinel[0].status).toBe('empty');
-    expect(sentinel[0].claim_text).toBe('');
-    const pending = await engine.executeRaw<{ n: number }>(
-      `SELECT COUNT(*)::int AS n FROM take_proposals WHERE page_slug = 'notes/zero-claims' AND status = 'pending'`,
-      [],
-    );
-    expect(Number(pending[0].n)).toBe(0);
-  });
-});
-
-describe('dropped claims — per-claim rows survive the idempotency index', () => {
-  test('a 3-claim page stores 3 rows and reports an honest inserted count', async () => {
-    const rows = await engine.executeRaw<{ claim_text: string }>(
-      `SELECT claim_text FROM take_proposals WHERE page_slug = 'notes/three-claims' AND status = 'pending' ORDER BY id`,
-      [],
-    );
-    // Pre-fix the 4-column unique index kept only the FIRST claim.
-    expect(rows.length).toBe(3);
-    expect(rows.map(r => r.claim_text)).toEqual([
-      'acme-example wins the market',
-      'widget-co will struggle',
-      'fund-a is overexposed',
-    ]);
-  });
-
-  test('content change re-extracts and stores the new version separately', async () => {
-    await engine.putPage('notes/zero-claims', {
-      type: 'note',
-      title: 'pure narrative',
-      compiled_truth: 'Updated: I now believe acme-example is undervalued and will re-rate within a year.',
-    });
-    const claims = {
-      'notes/zero-claims': [
-        { claim_text: 'acme-example is undervalued', kind: 'take' as const, holder: 'brain', weight: 0.6 },
-      ],
-    };
-    const run = countingExtractor(claims);
-    const r = await runPhaseProposeTakes(ctx(), { extractor: run.extractor });
-    expect(r.status).toBe('ok');
-    // Changed page re-extracts; the unchanged 3-claim page stays cached.
-    expect(run.calls).toEqual(['notes/zero-claims']);
-    expect((r.details as Record<string, unknown>).proposals_inserted).toBe(1);
-    const all = await engine.executeRaw<{ status: string }>(
-      `SELECT status FROM take_proposals WHERE page_slug = 'notes/zero-claims' ORDER BY id`,
-      [],
-    );
-    // Old hash's sentinel + new hash's pending claim coexist.
-    expect(all.map(r2 => r2.status).sort()).toEqual(['empty', 'pending']);
-  });
-});

test/propose-takes.test.ts

@@ -41,16 +41,12 @@ interface CapturedSql {
 function buildMockEngine(opts: {
   pages: Page[];
   existingProposals?: Set<string>; // composite-key strings already in take_proposals
-  config?: Record<string, string>; // engine.getConfig plane (models.tier.* etc.)
 }): { engine: BrainEngine; captured: CapturedSql[] } {
   const captured: CapturedSql[] = [];
   const existing = opts.existingProposals ?? new Set<string>();
 
   const engine = {
     kind: 'pglite',
-    async getConfig(key: string) {
-      return opts.config?.[key] ?? null;
-    },
     async listPages() {
       return opts.pages;
     },
@@ -63,12 +59,7 @@ function buildMockEngine(opts: {
         if (existing.has(key)) return [{ id: 1 } as unknown as T];
         return [];
       }
-      // INSERT ... RETURNING id — emulate a successful insert so the
-      // honest proposals_inserted counter (counts RETURNING rows, not
-      // attempts) sees the row land. Conflicted inserts would return [].
-      if (sql.includes('INSERT INTO take_proposals') && sql.includes('RETURNING id')) {
-        return [{ id: 1 } as unknown as T];
-      }
+      // INSERT — return nothing
       return [];
     },
   } as unknown as BrainEngine;
@@ -276,29 +267,6 @@ describe('runPhaseProposeTakes — phase integration', () => {
     expect(inserts[0]!.params[9]).toBe('market'); // domain
   });
 
-  test('extractor model resolves through models.propose_takes config', async () => {
-    // Pre-fix the phase's only model knob was the gateway chat model — there
-    // was no per-phase config key. The phase now resolves once via
-    // resolveModel(models.propose_takes > models.default > env > gateway
-    // chat model); the extractor hint and the stored model_id must both
-    // reflect the configured override (full provider-prefixed string, #2451).
-    const pages = [buildPage({ slug: 'wiki/concepts/tier-routing', body: 'Tier-routed models will win.' })];
-    const { engine, captured } = buildMockEngine({
-      pages,
-      config: { 'models.propose_takes': 'anthropic:claude-sonnet-5' },
-    });
-    const seen: Array<string | undefined> = [];
-    const extractor: ProposeTakesExtractor = async ({ modelHint }) => {
-      seen.push(modelHint);
-      return [{ claim_text: 'tier-routed models win', kind: 'bet', holder: 'brain', weight: 0.7 }];
-    };
-    const result = await runPhaseProposeTakes(buildCtx(engine), { extractor });
-    expect(result.status).toBe('ok');
-    expect(seen).toEqual(['anthropic:claude-sonnet-5']); // chat call gets the FULL string
-    const inserts = captured.filter(c => c.sql.includes('INSERT INTO take_proposals'));
-    expect(inserts[0]!.params[11]).toBe('anthropic:claude-sonnet-5'); // stored model_id matches the call
-  });
-
   test('cache hit: page already in take_proposals is skipped', async () => {
     const body = 'A page that was already processed.';
     const pages = [buildPage({ slug: 'wiki/old-page', body })];

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);
+  });
+});