fix(schema): block scalars keep '#' as literal content

Inside a YAML block scalar '#' is content, not a comment; parseBlockScalar
was routing lines through stripComment/isBlank, truncating descriptions
like 'see issue #2029' and blanking comment-looking lines. Use the raw
line inside the scalar. Adds a pinning test.

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

skills/article-enrichment/SKILL.md

@@ -85,10 +85,6 @@ 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

@@ -273,13 +273,6 @@ 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

@@ -1,62 +0,0 @@
-# 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

@@ -268,18 +268,6 @@ 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

@@ -270,11 +270,6 @@ 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', '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']);
+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']);
 // 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.
@@ -1652,11 +1652,6 @@ 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/reference.ts

@@ -1,130 +0,0 @@
-// 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/ai/anthropic-key.ts

@@ -18,12 +18,22 @@
 import { loadConfig } from '../config.ts';
 
 export function hasAnthropicKey(): boolean {
-  if (process.env.ANTHROPIC_API_KEY) return true;
+  return resolveAnthropicKey() !== undefined;
+}
+
+/**
+ * Resolve the actual key value: env first, then the gbrain config file.
+ * Callers constructing an Anthropic client directly (e.g. the legacy
+ * subagent path) must pass this as `apiKey` — a bare `new Anthropic()`
+ * only sees env, so launchd/MCP workers with config-stored keys fail.
+ */
+export function resolveAnthropicKey(): string | undefined {
+  if (process.env.ANTHROPIC_API_KEY) return process.env.ANTHROPIC_API_KEY;
   try {
     const cfg = loadConfig();
-    if (cfg?.anthropic_api_key) return true;
+    if (cfg?.anthropic_api_key) return cfg.anthropic_api_key;
   } catch {
     // loadConfig may throw on first-run installs; treat as no key available.
   }
-  return false;
+  return undefined;
 }

src/core/minions/handlers/subagent.ts

@@ -48,6 +48,7 @@ import {
   logSubagentHeartbeat,
 } from './subagent-audit.ts';
 import { resolveModel, isAnthropicProvider, TIER_DEFAULTS } from '../../model-config.ts';
+import { resolveAnthropicKey } from '../../ai/anthropic-key.ts';
 import { buildSystemPrompt, DEFAULT_SUBAGENT_SYSTEM } from '../system-prompt.ts';
 import { toolLoop as gatewayToolLoop } from '../../ai/gateway.ts';
 import type { ChatToolDef, ChatMessage, ChatBlock, ChatResult, ToolHandler } from '../../ai/gateway.ts';
@@ -186,7 +187,10 @@ export function makeSubagentHandler(deps: SubagentDeps) {
   // lives at sdk.messages.create. Assigning sdk.messages directly gets the
   // right object; JS method-call semantics preserve `this` at the call
   // site (subagent.ts invokes client.create(...) with client === sdk.messages).
-  const makeAnthropic = deps.makeAnthropic ?? (() => new Anthropic());
+  // Resolve the key env-first, then config (anthropic_api_key) — a bare
+  // new Anthropic() only reads env, so launchd/MCP workers whose key lives
+  // in the gbrain config file would fail auth (#2048).
+  const makeAnthropic = deps.makeAnthropic ?? (() => new Anthropic({ apiKey: resolveAnthropicKey() }));
   const client: MessagesClient = deps.client ?? makeAnthropic().messages;
   const config = deps.config ?? loadConfig() ?? ({ engine: 'postgres' } as GBrainConfig);
   const rateLeaseKey = deps.rateLeaseKey ?? DEFAULT_RATE_KEY;

src/core/onboard/checks.ts

@@ -18,7 +18,6 @@
 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 {
@@ -121,8 +120,7 @@ export async function checkEntityLinkCoverage(
     engine,
     `SELECT COUNT(*) AS count FROM pages
        WHERE type IN ('person', 'company', 'organization', 'entity')
-         AND deleted_at IS NULL
-         AND ${referenceExclusionSql()}`,
+         AND deleted_at IS NULL`,
   );
 
   if (totalEntities === 0) {
@@ -146,7 +144,6 @@ 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`,
   );
@@ -218,8 +215,7 @@ export async function checkTimelineCoverage(
     engine,
     `SELECT COUNT(*) AS count FROM pages
        WHERE type IN ('person', 'company', 'organization', 'entity')
-         AND deleted_at IS NULL
-         AND ${referenceExclusionSql()}`,
+         AND deleted_at IS NULL`,
   );
 
   if (totalEntities === 0) {
@@ -241,7 +237,6 @@ 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

@@ -14,7 +14,6 @@
 // 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;
 
@@ -58,8 +57,7 @@ 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 ${referenceExclusionSql()}`,
+             AND deleted_at IS NULL`,
         [],
         { signal: controller.signal },
       ),
@@ -67,7 +65,6 @@ 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 },
@@ -76,7 +73,6 @@ 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

@@ -4562,7 +4562,8 @@ const list_schema_packs: Operation = {
     const { existsSync, readdirSync } = await import('node:fs');
     const { join } = await import('node:path');
     const { gbrainPath } = await import('./config.ts');
-    const bundled = ['gbrain-base', 'gbrain-recommended'];
+    const { BUNDLED_PACK_NAMES } = await import('./schema-pack/bundled.ts');
+    const bundled = [...BUNDLED_PACK_NAMES];
     const installedDir = gbrainPath('schema-packs');
     const installed: string[] = [];
     if (existsSync(installedDir)) {

src/core/pglite-engine.ts

@@ -23,7 +23,6 @@ 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';
@@ -5203,7 +5202,6 @@ 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

@@ -5320,12 +5320,7 @@ 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

@@ -1,37 +0,0 @@
-// 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-pack/bundled.ts

@@ -0,0 +1,24 @@
+// Bundled schema-pack registry — single source of truth for the packs that
+// ship in src/core/schema-pack/base/. Keep every bundled-pack consumer
+// (CLI/MCP inspection, active-pack loading, mutation guards, upgrade
+// discovery) on this one list so they cannot drift.
+//
+// v0.39 T8 — gbrain-base + gbrain-recommended.
+// v0.41 T4 — lens packs: creator, investor, engineer, everything (meta-pack).
+// v0.42 type-unification — gbrain-base-v2, the 15-type canonical successor.
+
+export const BUNDLED_PACK_NAMES = [
+  'gbrain-base',
+  'gbrain-recommended',
+  'gbrain-creator',
+  'gbrain-investor',
+  'gbrain-engineer',
+  'gbrain-everything',
+  'gbrain-base-v2',
+] as const;
+
+export type BundledPackName = typeof BUNDLED_PACK_NAMES[number];
+
+export function isBundledPackName(name: string): name is BundledPackName {
+  return (BUNDLED_PACK_NAMES as readonly string[]).includes(name);
+}

src/core/schema-pack/load-active.ts

@@ -37,6 +37,7 @@ import {
   type ResolutionInput,
   type ResolutionResult,
 } from './registry.ts';
+import { isBundledPackName } from './bundled.ts';
 
 /**
  * Inputs the caller (operations.ts handler / engine query path) provides.
@@ -92,28 +93,7 @@ export function _resetPackLocatorForTests(): void {
  * throwing UnknownPackError with a paste-ready install hint.
  */
 function defaultPackLocator(name: string): string | null {
-  // v0.39 T8 — bundled packs registry. gbrain-base + gbrain-recommended
-  // ship in src/core/schema-pack/base/. Add a new entry here to bundle
-  // additional canonical packs.
-  //
-  // v0.41 T4 — lens packs join the bundle: creator (atoms + concepts +
-  // extract_atoms/synthesize_concepts phases), investor (theses + bet
-  // resolution + 3 calibration domains), engineer (gstack-learnings bridge
-  // + 3 calibration domains), everything (meta-pack stacking all three
-  // via extends + borrow_from). Each ships as a real YAML at base/<name>.yaml.
-  const BUNDLED: ReadonlyArray<string> = [
-    'gbrain-base',
-    'gbrain-recommended',
-    'gbrain-creator',
-    'gbrain-investor',
-    'gbrain-engineer',
-    'gbrain-everything',
-    // v0.42 type-unification: 15-type canonical successor to gbrain-base.
-    // Ships as install default (Lane E T17) + via gbrain onboard pack
-    // upgrade flow (the unify-types Minion handler).
-    'gbrain-base-v2',
-  ];
-  if (BUNDLED.includes(name)) {
+  if (isBundledPackName(name)) {
     // Resolve bundled YAML relative to this source file. Works in both
     // direct-bun execution and bun --compile binaries.
     const here = dirname(fileURLToPath(import.meta.url));

src/core/schema-pack/loader.ts

@@ -159,6 +159,29 @@ export function parseYamlMini(content: string): unknown {
     return parseMapping(baseIndent);
   }
 
+  function parseBlockScalar(parentIndent: number, folded: boolean): string {
+    const contentIndent = parentIndent + 2;
+    const out: string[] = [];
+    while (i < lines.length) {
+      const raw = lines[i];
+      // Inside a block scalar everything is literal content — '#' is NOT a
+      // comment here, so use the raw line (no stripComment / isBlank).
+      if (raw.trim() === '') {
+        out.push('');
+        i++;
+        continue;
+      }
+      const indent = indentOf(raw);
+      if (indent <= parentIndent) break;
+      out.push(raw.slice(Math.min(contentIndent, indent)));
+      i++;
+    }
+    if (folded) {
+      return out.join(' ').replace(/\s+$/u, '');
+    }
+    return out.join('\n').replace(/\n+$/u, '');
+  }
+
   function parseSequence(baseIndent: number): unknown[] {
     const result: unknown[] = [];
     while (i < lines.length) {
@@ -227,6 +250,10 @@ export function parseYamlMini(content: string): unknown {
           i++;
           if (rest2 === '') {
             map[key2] = parseBlock(nextIndent + 2);
+          } else if (rest2 === '|' || rest2 === '|-' || rest2 === '|+') {
+            map[key2] = parseBlockScalar(nextIndent, false);
+          } else if (rest2 === '>' || rest2 === '>-' || rest2 === '>+') {
+            map[key2] = parseBlockScalar(nextIndent, true);
           } else {
             map[key2] = parseScalar(rest2);
           }
@@ -257,6 +284,10 @@ export function parseYamlMini(content: string): unknown {
       i++;
       if (rest === '') {
         result[key] = parseBlock(indent + 2);
+      } else if (rest === '|' || rest === '|-' || rest === '|+') {
+        result[key] = parseBlockScalar(indent, false);
+      } else if (rest === '>' || rest === '>-' || rest === '>+') {
+        result[key] = parseBlockScalar(indent, true);
       } else {
         result[key] = parseScalar(rest);
       }

src/core/schema-pack/mutate.ts

@@ -65,6 +65,7 @@ import { invalidateQueryCache } from './query-cache-invalidator.ts';
 import { logMutationFailure, logMutationSuccess, type MutationActor, type MutationOp } from './mutate-audit.ts';
 import { runFilePlaneLintRules } from './lint-rules.ts';
 import { withPackLock, type PackLockOpts } from './pack-lock.ts';
+import { BUNDLED_PACK_NAMES as BUNDLED_PACK_NAME_LIST } from './bundled.ts';
 import type { BrainEngine } from '../engine.ts';
 
 export type PackFileFormat = 'json' | 'yaml';
@@ -93,7 +94,7 @@ export class SchemaPackMutationError extends Error {
   }
 }
 
-export const BUNDLED_PACK_NAMES = new Set(['gbrain-base', 'gbrain-recommended', 'gbrain-base-v2']);
+export const BUNDLED_PACK_NAMES = new Set<string>(BUNDLED_PACK_NAME_LIST);
 
 export interface MutateResult {
   /** Pack name that was mutated. */

test/ai/anthropic-key.test.ts

@@ -10,7 +10,7 @@ import { mkdtempSync, mkdirSync, writeFileSync, rmSync } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 import { withEnv } from '../helpers/with-env.ts';
-import { hasAnthropicKey } from '../../src/core/ai/anthropic-key.ts';
+import { hasAnthropicKey, resolveAnthropicKey } from '../../src/core/ai/anthropic-key.ts';
 
 const tmpDirs: string[] = [];
 function freshHome(withConfig?: Record<string, unknown>): string {
@@ -62,3 +62,35 @@ describe('hasAnthropicKey', () => {
     );
   });
 });
+
+describe('resolveAnthropicKey (#2048 — subagent config-key auth)', () => {
+  test('env wins over config', async () => {
+    const home = freshHome({ anthropic_api_key: 'sk-from-config' });
+    await withEnv(
+      { ANTHROPIC_API_KEY: 'sk-from-env', GBRAIN_HOME: home, DATABASE_URL: undefined, GBRAIN_DATABASE_URL: undefined },
+      async () => {
+        expect(resolveAnthropicKey()).toBe('sk-from-env');
+      },
+    );
+  });
+
+  test('config key returned when env unset', async () => {
+    const home = freshHome({ anthropic_api_key: 'sk-from-config' });
+    await withEnv(
+      { ANTHROPIC_API_KEY: undefined, GBRAIN_HOME: home, DATABASE_URL: undefined, GBRAIN_DATABASE_URL: undefined },
+      async () => {
+        expect(resolveAnthropicKey()).toBe('sk-from-config');
+      },
+    );
+  });
+
+  test('neither → undefined', async () => {
+    const home = freshHome();
+    await withEnv(
+      { ANTHROPIC_API_KEY: undefined, GBRAIN_HOME: home, DATABASE_URL: undefined, GBRAIN_DATABASE_URL: undefined },
+      async () => {
+        expect(resolveAnthropicKey()).toBeUndefined();
+      },
+    );
+  });
+});

test/lens-pack-manifests.test.ts

@@ -55,13 +55,13 @@ describe('v0.41 T4: all 4 bundled lens packs parse cleanly', () => {
 });
 
 describe('v0.41 T4: bundled registry includes lens packs', () => {
-  test('load-active.ts BUNDLED array source includes the 4 lens pack names', () => {
-    const loadActiveSrc = readFileSync(
-      join(here, '..', 'src', 'core', 'schema-pack', 'load-active.ts'),
-      'utf-8',
-    );
+  test('BUNDLED_PACK_NAMES includes the 4 lens pack names', async () => {
+    // The bundled list moved from load-active.ts to bundled.ts (the
+    // single source of truth); assert the array directly instead of
+    // grepping source text.
+    const { BUNDLED_PACK_NAMES } = await import('../src/core/schema-pack/bundled.ts');
     for (const name of PACK_NAMES) {
-      expect(loadActiveSrc).toContain(`'${name}'`);
+      expect(BUNDLED_PACK_NAMES).toContain(name);
     }
   });
 });

test/operations-schema-pack.test.ts

@@ -149,6 +149,9 @@ describe('list_schema_packs', () => {
       seedPack('mine');
       const result = await operationsByName.list_schema_packs!.handler(ctxOf(), {}) as { bundled: string[]; installed: string[] };
       expect(result.bundled).toContain('gbrain-base');
+      expect(result.bundled).toContain('gbrain-recommended');
+      expect(result.bundled).toContain('gbrain-base-v2');
+      expect(result.bundled).toContain('gbrain-investor');
       expect(result.installed).toContain('mine');
     });
   });

test/reference-flag.test.ts

@@ -1,154 +0,0 @@
-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);
-  });
-});

test/schema-cli.test.ts

@@ -64,11 +64,14 @@ describe('gbrain schema CLI (Phase C)', () => {
     expect(r.stdout + r.stderr).toMatch(/schema|active|list|show|validate|use/i);
   });
 
-  test('schema list shows gbrain-base bundled', () => {
+  test('schema list shows all bundled packs', () => {
     const r = gbrain(['schema', 'list']);
     expect(r.code).toBe(0);
     expect(r.stdout).toContain('Bundled packs:');
     expect(r.stdout).toContain('gbrain-base');
+    expect(r.stdout).toContain('gbrain-recommended');
+    expect(r.stdout).toContain('gbrain-base-v2');
+    expect(r.stdout).toContain('gbrain-investor');
   });
 
   test('schema show gbrain-base prints manifest details', () => {
@@ -97,6 +100,40 @@ describe('gbrain schema CLI (Phase C)', () => {
     expect(r.stdout).toContain('valid manifest');
   });
 
+  test('schema show/validate exposes bundled gbrain-recommended', () => {
+    const show = gbrain(['schema', 'show', 'gbrain-recommended']);
+    expect(show.code).toBe(0);
+    expect(show.stdout).toContain('gbrain-recommended v1.0.0');
+    expect(show.stdout).toContain('Page types (');
+    expect(show.stdout).toContain('meeting :: temporal');
+
+    const validate = gbrain(['schema', 'validate', 'gbrain-recommended']);
+    expect(validate.code).toBe(0);
+    expect(validate.stdout).toContain('valid manifest');
+  });
+
+  test('schema show exposes bundled gbrain-base-v2 successor pack', () => {
+    const r = gbrain(['schema', 'show', 'gbrain-base-v2']);
+    expect(r.code).toBe(0);
+    expect(r.stdout).toContain('gbrain-base-v2 v1.0.0');
+    expect(r.stdout).toContain('Page types (');
+    expect(r.stdout).toContain('Link verbs (14)');
+  });
+
+  test('schema active loads configured gbrain-recommended with real types', () => {
+    const home = mkdtempSync(join(tmpdir(), 'gbrain-schema-active-recommended-'));
+    try {
+      mkdirSync(join(home, '.gbrain'), { recursive: true });
+      writeFileSync(join(home, '.gbrain', 'config.json'), JSON.stringify({ schema_pack: 'gbrain-recommended' }), 'utf-8');
+      const r = gbrain(['schema', 'active'], { GBRAIN_HOME: home });
+      expect(r.code).toBe(0);
+      expect(r.stdout).toContain('Active pack: gbrain-recommended');
+      expect(r.stdout).not.toContain('Page types: 0');
+    } finally {
+      rmSync(home, { recursive: true, force: true });
+    }
+  });
+
   test('schema active reports default resolution', () => {
     const r = gbrain(['schema', 'active']);
     expect(r.code).toBe(0);

test/schema-pack-loader.test.ts

@@ -345,6 +345,34 @@ describe('YAML mini-parser', () => {
     expect(result.types[1].weight).toBe(2);
   });
 
+  test('parses block scalar without swallowing following keys', () => {
+    const yaml = `name: blocky
+description: |
+  First line.
+  Second line.
+page_types:
+  - name: meeting
+    primitive: temporal
+    path_prefixes:
+      - meetings/
+    aliases: []
+    extractable: true
+    expert_routing: false`;
+    const result = parseYamlMini(yaml) as { description: string; page_types: Array<Record<string, unknown>> };
+    expect(result.description).toBe('First line.\nSecond line.');
+    expect(result.page_types).toHaveLength(1);
+    expect(result.page_types[0].name).toBe('meeting');
+  });
+
+  test('block scalar keeps # as literal content, not a comment', () => {
+    const yaml = `description: |
+  See issue #2029 for context.
+name: hashy`;
+    const result = parseYamlMini(yaml) as Record<string, unknown>;
+    expect(result.description).toBe('See issue #2029 for context.');
+    expect(result.name).toBe('hashy');
+  });
+
   test('strips comments', () => {
     const result = parseYamlMini('# top comment\nname: value # inline comment') as Record<string, unknown>;
     expect(result.name).toBe('value');
@@ -374,6 +402,27 @@ extends: null`;
     const pack = loadPackFromString(json, 'fixture.json');
     expect(pack.name).toBe('json-pack');
   });
+
+  test('loads block-scalar pack descriptions without losing page types', () => {
+    const pack = loadPackFromString(`api_version: gbrain-schema-pack-v1
+name: recommended-fixture
+version: 1.0.0
+extends: gbrain-base
+description: |
+  Operational starter pack.
+page_types:
+  - name: meeting
+    primitive: temporal
+    path_prefixes:
+      - meetings/
+    aliases: []
+    extractable: true
+    expert_routing: false
+link_types: []`, 'fixture.yaml');
+    expect(pack.name).toBe('recommended-fixture');
+    expect(pack.extends).toBe('gbrain-base');
+    expect(pack.page_types.map((t) => t.name)).toContain('meeting');
+  });
 });
 
 describe('ReDoS guard', () => {

test/schema-pack-mutate.test.ts

@@ -103,7 +103,10 @@ describe('locateMutablePackFile — bundled guard', () => {
     expect(BUNDLED_PACK_NAMES.has('gbrain-recommended')).toBe(true);
     // v0.42 (T22): gbrain-base-v2 joins the bundled set.
     expect(BUNDLED_PACK_NAMES.has('gbrain-base-v2')).toBe(true);
-    expect(BUNDLED_PACK_NAMES.size).toBe(3);
+    // Derived from the single bundled registry — the lens packs (creator,
+    // investor, engineer, everything) are read-only too.
+    expect(BUNDLED_PACK_NAMES.has('gbrain-investor')).toBe(true);
+    expect(BUNDLED_PACK_NAMES.size).toBe(7);
   });
 
   it('rejects gbrain-base-v2 with PACK_READONLY (bundled guard)', () => {