fix(admin): source scoping + redirect URIs in admin OAuth registration

Takeover of #1558 (rebased onto master, admin/dist + admin-embedded regenerated so asset hashes match; source changes salvaged intact): - /admin/api/register-client now accepts source_id + federated_read (snake and camel case), validated fail-closed against the registered source list via the new normalizeAdminClientSourceScope (src/core/admin-source-scope.ts) before reaching registerClientManual — unknown or malformed ids are a 400, never a silently-hardcoded 'default'. Fixes #1490. - New requireAdmin-gated GET /admin/api/sources feeds the Register Agent form; the form now has a Write Source select + Read Sources checkboxes, and the agents table/drawer show each client's scope. - #1036: the Register Agent form now has a Redirect URIs textarea (one per line). When present, the POST carries redirectUris plus the authorization_code + refresh_token grants, mirroring the CLI's --redirect-uri grant-inference convention (src/commands/auth.ts). Backend plumbing already existed; this was UI-only. Tests: test/admin-source-scope.test.ts (normalization matrix), test/oauth.test.ts (registerClientManual persists source scope into AuthInfo), test/fix-wave-structural.test.ts (endpoint + form pins for #1490 and #1036). Co-authored-by: flamerged <flamerged@users.noreply.github.com> Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-08-16 18:02:30 +00:00 · 2026-07-21 15:09:32 -07:00
25 changed files with 330 additions and 499 deletions
@@ -7,7 +7,7 @@
  <link rel="preconnect" href="https://fonts.googleapis.com" />
  <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin />
  <link href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600&family=JetBrains+Mono:wght@400;500&display=swap" rel="stylesheet" />
-  <script type="module" crossorigin src="/admin/assets/index-CoGEje3-.js"></script>
+  <script type="module" crossorigin src="/admin/assets/index-CzLjRij_.js"></script>
  <link rel="stylesheet" crossorigin href="/admin/assets/index-GxkWX7v3.css">
 </head>
 <body>
@@ -39,6 +39,7 @@ export const api = {
  stats: () => apiFetch('/admin/api/stats'),
  health: () => apiFetch('/admin/api/health-indicators'),
  agents: () => apiFetch('/admin/api/agents'),
+  sources: () => apiFetch('/admin/api/sources'),
  requests: (page = 1, qs = '') => apiFetch(`/admin/api/requests?page=${page}${qs}`),
  apiKeys: () => apiFetch('/admin/api/api-keys'),
  createApiKey: (name: string) => apiFetch('/admin/api/api-keys', { method: 'POST', body: JSON.stringify({ name }) }),
@@ -23,9 +23,16 @@ interface Agent {
  total_requests: number;
  requests_today: number;
  token_ttl: number | null;
+  source_id: string | null;
+  federated_read: string[] | null;
  status: 'active' | 'revoked';
 }

+interface SourceOption {
+  id: string;
+  name: string | null;
+}
+
 interface ApiKey {
  id: string;
  name: string;
@@ -88,6 +95,7 @@ export function AgentsPage() {
                <th>Name</th>
                <th>Type</th>
                <th>Scopes</th>
+                <th>Source</th>
                <th>Status</th>
                <th>Requests</th>
                <th>Last Used</th>
@@ -108,6 +116,9 @@ export function AgentsPage() {
                      <span key={s} className={`badge badge-${s}`} style={{ marginRight: 4 }}>{s}</span>
                    ))}
                  </td>
+                  <td className="mono" style={{ fontSize: 12, color: 'var(--text-secondary)' }}>
+                    {a.auth_type === 'oauth' ? (a.source_id || 'default') : 'all'}
+                  </td>
                  <td>
                    <span className={`badge ${a.status === 'active' ? 'badge-success' : 'badge-danger'}`}>{a.status}</span>
                  </td>
@@ -257,9 +268,29 @@ function RegisterModal({ onClose, onRegistered }: {
    Object.fromEntries(ALLOWED_SCOPES_LIST.map(s => [s, s === 'read'])) as Record<Scope, boolean>,
  );
  const [ttl, setTtl] = useState('86400'); // 24h default
+  const [redirectUris, setRedirectUris] = useState('');
+  const [sources, setSources] = useState<SourceOption[]>([{ id: 'default', name: 'default' }]);
+  const [sourceId, setSourceId] = useState('default');
+  const [readSources, setReadSources] = useState<Record<string, boolean>>({ default: true });
  const [loading, setLoading] = useState(false);
  const [error, setError] = useState('');

+  useEffect(() => {
+    api.sources()
+      .then((rows: SourceOption[]) => {
+        const nextSources = rows.length > 0 ? rows : [{ id: 'default', name: 'default' }];
+        const nextSourceId = nextSources.some(s => s.id === sourceId) ? sourceId : nextSources[0].id;
+        setSources(nextSources);
+        setSourceId(nextSourceId);
+        setReadSources(prev => {
+          const next = Object.fromEntries(nextSources.map(s => [s.id, Boolean(prev[s.id])])) as Record<string, boolean>;
+          next[nextSourceId] = true;
+          return next;
+        });
+      })
+      .catch(() => {});
+  }, []);
+
  const ttlOptions = [
    { label: '1 hour', value: '3600' },
    { label: '24 hours', value: '86400' },
@@ -277,11 +308,24 @@ function RegisterModal({ onClose, onRegistered }: {
    try {
      // Use the CLI registration endpoint (POST to admin API)
      const selectedScopes = Object.entries(scopes).filter(([, v]) => v).map(([k]) => k).join(' ');
+      const federatedRead = sources.map(s => s.id).filter(id => readSources[id]);
+      if (federatedRead.length === 0) { setError('Select at least one read source'); setLoading(false); return; }
+      // #1036: redirect URIs, one per line. Mirrors the CLI convention
+      // (src/commands/auth.ts): presence of redirect URIs implies
+      // authorization_code + refresh_token grants unless the user had none.
+      const uris = redirectUris.split('\n').map(u => u.trim()).filter(Boolean);
      const res = await fetch('/admin/api/register-client', {
        method: 'POST',
        credentials: 'same-origin',
        headers: { 'Content-Type': 'application/json' },
-        body: JSON.stringify({ name: name.trim(), scopes: selectedScopes, tokenTtl: ttl === '0' ? 315360000 : Number(ttl) }),
+        body: JSON.stringify({
+          name: name.trim(),
+          scopes: selectedScopes,
+          tokenTtl: ttl === '0' ? 315360000 : Number(ttl),
+          source_id: sourceId,
+          federated_read: federatedRead,
+          ...(uris.length > 0 ? { redirectUris: uris, grantTypes: ['authorization_code', 'refresh_token'] } : {}),
+        }),
      });
      if (!res.ok) throw new Error('Registration failed');
      const data = await res.json();
@@ -312,6 +356,42 @@ function RegisterModal({ onClose, onRegistered }: {
            ))}
          </div>
        </div>
+        <div style={{ marginBottom: 16 }}>
+          <label>Write Source</label>
+          <select value={sourceId} onChange={e => {
+            const id = e.target.value;
+            setSourceId(id);
+            setReadSources(p => ({ ...p, [id]: true }));
+          }}
+            style={{ width: '100%', background: 'var(--bg-secondary)', color: 'var(--text-primary)', border: '1px solid var(--border)', borderRadius: 6, padding: '6px 10px', fontSize: 14 }}>
+            {sources.map(s => <option key={s.id} value={s.id}>{s.name && s.name !== s.id ? `${s.id} (${s.name})` : s.id}</option>)}
+          </select>
+        </div>
+        <div style={{ marginBottom: 16 }}>
+          <label>Read Sources</label>
+          <div className="checkbox-group">
+            {sources.map(s => (
+              <label key={s.id} className="checkbox-label">
+                <input
+                  type="checkbox"
+                  checked={Boolean(readSources[s.id])}
+                  onChange={e => setReadSources(p => ({ ...p, [s.id]: e.target.checked }))}
+                />
+                {s.name && s.name !== s.id ? `${s.id} (${s.name})` : s.id}
+              </label>
+            ))}
+          </div>
+        </div>
+        <div style={{ marginBottom: 16 }}>
+          <label>Redirect URIs <span style={{ color: 'var(--text-secondary)', fontWeight: 400 }}>(optional, one per line — enables authorization_code flow)</span></label>
+          <textarea
+            placeholder={'https://example.com/callback'}
+            value={redirectUris}
+            onChange={e => setRedirectUris(e.target.value)}
+            rows={2}
+            style={{ width: '100%', background: 'var(--bg-secondary)', color: 'var(--text-primary)', border: '1px solid var(--border)', borderRadius: 6, padding: '6px 10px', fontSize: 13, fontFamily: 'inherit', resize: 'vertical' }}
+          />
+        </div>
        <div style={{ marginBottom: 20 }}>
          <label>Token Lifetime</label>
          <select value={ttl} onChange={e => setTtl(e.target.value)}
@@ -528,6 +608,8 @@ function AgentDrawer({ agent, onClose, onRevoked }: { agent: Agent; onClose: ()
      client_name: agentName,
      auth_type: agent.auth_type,
      scope: agent.scope,
+      source_id: agent.source_id,
+      federated_read: agent.federated_read,
    }, null, 2),
  };

@@ -547,6 +629,10 @@ function AgentDrawer({ agent, onClose, onRevoked }: { agent: Agent; onClose: ()
          <span>{(agent.scope || '').split(' ').filter(Boolean).map(s => (
            <span key={s} className={`badge badge-${s}`} style={{ marginRight: 4 }}>{s}</span>
          ))}</span>
+          <span style={{ color: 'var(--text-secondary)' }}>Write Source</span>
+          <span className="mono">{agent.source_id || (isOAuth ? 'default' : 'all')}</span>
+          <span style={{ color: 'var(--text-secondary)' }}>Read Sources</span>
+          <span className="mono">{isOAuth ? (agent.federated_read && agent.federated_read.length > 0 ? agent.federated_read.join(', ') : (agent.source_id || 'default')) : 'all'}</span>
          <span style={{ color: 'var(--text-secondary)' }}>Registered</span>
          <span>{new Date(agent.created_at).toLocaleDateString()}</span>
          <span style={{ color: 'var(--text-secondary)' }}>Token TTL</span>
@@ -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
@@ -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)

@@ -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`.
@@ -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)
@@ -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`.
@@ -1,13 +1,13 @@
 // AUTO-GENERATED — do not edit by hand.
 // Run `bun run scripts/build-admin-embedded.ts` to regenerate.
-// Source: admin/dist/ at 2026-05-27.
+// Source: admin/dist/ at 2026-07-21.
 //
 // Bun resolves the file: imports to a path that works at runtime even
 // inside a compiled binary (`bun build --compile`). The manifest maps
 // the request path the express handler sees to (resolved-path, mime).

 // @ts-ignore — type: 'file' is Bun ESM, not in lib.d.ts
-import A_0_assets_index_CoGEje3__js from '../admin/dist/assets/index-CoGEje3-.js' with { type: 'file' };
+import A_0_assets_index_CzLjRij__js from '../admin/dist/assets/index-CzLjRij_.js' with { type: 'file' };
 // @ts-ignore — type: 'file' is Bun ESM, not in lib.d.ts
 import A_1_assets_index_GxkWX7v3_css from '../admin/dist/assets/index-GxkWX7v3.css' with { type: 'file' };
 // @ts-ignore — type: 'file' is Bun ESM, not in lib.d.ts
@@ -19,7 +19,7 @@ export interface AdminAsset {
 }

 export const ADMIN_ASSETS: Record<string, AdminAsset> = {
-  "/admin/assets/index-CoGEje3-.js": { path: A_0_assets_index_CoGEje3__js as unknown as string, mime: "application/javascript; charset=utf-8" },
+  "/admin/assets/index-CzLjRij_.js": { path: A_0_assets_index_CzLjRij__js as unknown as string, mime: "application/javascript; charset=utf-8" },
  "/admin/assets/index-GxkWX7v3.css": { path: A_1_assets_index_GxkWX7v3_css as unknown as string, mime: "text/css; charset=utf-8" },
  "/admin/index.html": { path: A_2_index_html as unknown as string, mime: "text/html; charset=utf-8" },
 };
@@ -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);
@@ -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.');
-    }
-  }
-}
@@ -39,6 +39,7 @@ import * as db from '../core/db.ts';
 import { sqlQueryForEngine, executeRawJsonb } from '../core/sql-query.ts';
 import { MinionQueue } from '../core/minions/queue.ts';
 import { isRetryableError } from '../core/retry-matcher.ts';
+import { normalizeAdminClientSourceScope } from '../core/admin-source-scope.ts';
 import {
  computeContentHash,
  validateIngestionEvent,
@@ -1086,6 +1087,7 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
      const oauthClients = await sql`
        SELECT c.client_id as id, c.client_name as name, 'oauth' as auth_type,
          c.grant_types, c.scope, c.created_at, c.token_ttl,
+          c.source_id, c.federated_read,
          CASE WHEN c.deleted_at IS NOT NULL THEN 'revoked' ELSE 'active' END as status,
          (SELECT max(created_at) FROM mcp_request_log WHERE token_name = c.client_id) as last_used_at,
          (SELECT count(*)::int FROM mcp_request_log WHERE token_name = c.client_id) as total_requests,
@@ -1095,6 +1097,7 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
      const legacyKeys = await sql`
        SELECT a.id, a.name, 'api_key' as auth_type,
          '{"bearer"}' as grant_types, 'read write admin' as scope, a.created_at, null as token_ttl,
+          null as source_id, null as federated_read,
          CASE WHEN a.revoked_at IS NOT NULL THEN 'revoked' ELSE 'active' END as status,
          a.last_used_at,
          (SELECT count(*)::int FROM mcp_request_log WHERE token_name = a.name) as total_requests,
@@ -1107,6 +1110,17 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
    }
  });

+  app.get('/admin/api/sources', requireAdmin, async (_req: Request, res: Response) => {
+    try {
+      const sources = await engine.listAllSources({ includeArchived: false });
+      const options = sources.map(s => ({ id: s.id, name: s.name }));
+      if (!options.some(s => s.id === 'default')) options.unshift({ id: 'default', name: 'default' });
+      res.json(options);
+    } catch (e) {
+      res.status(503).json({ error: 'service_unavailable' });
+    }
+  });
+
  // v0.38 Slice 4 — per-OAuth-client agent spend viewer. Pre-computes today's
  // spend (committed + pending reservations) per client so the Agents tab
  // can render a "$X / $Y today" cell. Read-side endpoint only — no mutation.
@@ -1440,6 +1454,8 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
      // missing, empty) and rejects the rest with a structured 400.
      const { name, tokenTtl, grantTypes, redirectUris, tokenEndpointAuthMethod } = req.body;
      const rawScopes = (req.body as Record<string, unknown>).scopes ?? (req.body as Record<string, unknown>).scope;
+      const rawSourceId = (req.body as Record<string, unknown>).source_id ?? (req.body as Record<string, unknown>).sourceId;
+      const rawFederatedRead = (req.body as Record<string, unknown>).federated_read ?? (req.body as Record<string, unknown>).federatedRead;
      if (!name) { res.status(400).json({ error: 'Name required' }); return; }
      let scopeString: string;
      try {
@@ -1470,8 +1486,23 @@ export async function runServeHttp(engine: BrainEngine, options: ServeHttpOption
        });
        return;
      }
+      let sourceScope: ReturnType<typeof normalizeAdminClientSourceScope>;
+      try {
+        const sources = await engine.listAllSources({ includeArchived: false });
+        sourceScope = normalizeAdminClientSourceScope(
+          rawSourceId,
+          rawFederatedRead,
+          sources.map(s => s.id),
+        );
+      } catch (e) {
+        res.status(400).json({
+          error: 'invalid_source_scope',
+          message: e instanceof Error ? e.message : String(e),
+        });
+        return;
+      }
      const result = await oauthProvider.registerClientManual(
-        name, grants, scopeString, uris, 'default', undefined, validatedAuthMethod,
+        name, grants, scopeString, uris, sourceScope.sourceId, sourceScope.federatedRead, validatedAuthMethod,
      );
      // Set per-client TTL if specified
      if (tokenTtl && Number(tokenTtl) > 0) {
@@ -0,0 +1,51 @@
+import { isValidSourceId } from './source-id.ts';
+
+export interface AdminClientSourceScope {
+  sourceId: string;
+  federatedRead: string[];
+}
+
+function parseFederatedReadInput(raw: unknown, sourceId: string): string[] {
+  if (raw === undefined || raw === null) return [sourceId];
+  if (typeof raw === 'string') {
+    const values = raw.split(',').map(s => s.trim()).filter(Boolean);
+    return values.length > 0 ? values : [sourceId];
+  }
+  if (Array.isArray(raw)) {
+    if (!raw.every(v => typeof v === 'string')) {
+      throw new Error('federated_read must be an array of source ids');
+    }
+    const values = raw.map(v => v.trim()).filter(Boolean);
+    return values.length > 0 ? values : [sourceId];
+  }
+  throw new Error('federated_read must be a string or array');
+}
+
+export function normalizeAdminClientSourceScope(
+  rawSourceId: unknown,
+  rawFederatedRead: unknown,
+  availableSourceIds: string[],
+): AdminClientSourceScope {
+  const knownSources = new Set(availableSourceIds);
+  const fallbackSourceId = knownSources.has('default') ? 'default' : (availableSourceIds[0] ?? 'default');
+  const sourceId = rawSourceId === undefined || rawSourceId === null || rawSourceId === ''
+    ? fallbackSourceId
+    : rawSourceId;
+  if (!isValidSourceId(sourceId)) {
+    throw new Error(`Invalid source_id: ${JSON.stringify(sourceId)}`);
+  }
+  if (knownSources.size > 0 && !knownSources.has(sourceId)) {
+    throw new Error(`Unknown source_id: ${sourceId}`);
+  }
+
+  const federatedRead = Array.from(new Set(parseFederatedReadInput(rawFederatedRead, sourceId)));
+  for (const id of federatedRead) {
+    if (!isValidSourceId(id)) {
+      throw new Error(`Invalid federated_read source_id: ${JSON.stringify(id)}`);
+    }
+    if (knownSources.size > 0 && !knownSources.has(id)) {
+      throw new Error(`Unknown federated_read source_id: ${id}`);
+    }
+  }
+  return { sourceId, federatedRead };
+}
@@ -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`,
  );
@@ -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 },
@@ -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,
@@ -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,
@@ -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'`;
-}
@@ -0,0 +1,44 @@
+import { describe, expect, test } from 'bun:test';
+import { normalizeAdminClientSourceScope } from '../src/core/admin-source-scope.ts';
+
+describe('admin register-client source scope normalization', () => {
+  const sources = ['default', 'team-a', 'team-b'];
+
+  test('defaults write and read scope to default source', () => {
+    expect(normalizeAdminClientSourceScope(undefined, undefined, sources)).toEqual({
+      sourceId: 'default',
+      federatedRead: ['default'],
+    });
+  });
+
+  test('accepts snake-case body fields with multiple read sources', () => {
+    expect(normalizeAdminClientSourceScope('team-a', ['team-a', 'team-b'], sources)).toEqual({
+      sourceId: 'team-a',
+      federatedRead: ['team-a', 'team-b'],
+    });
+  });
+
+  test('accepts comma-separated federated_read for API callers', () => {
+    expect(normalizeAdminClientSourceScope('team-a', 'team-b, default,team-b', sources)).toEqual({
+      sourceId: 'team-a',
+      federatedRead: ['team-b', 'default'],
+    });
+  });
+
+  test('falls back to selected write source when federated_read is empty', () => {
+    expect(normalizeAdminClientSourceScope('team-b', [], sources)).toEqual({
+      sourceId: 'team-b',
+      federatedRead: ['team-b'],
+    });
+  });
+
+  test('rejects malformed source ids before registration', () => {
+    expect(() => normalizeAdminClientSourceScope('../secret', undefined, sources)).toThrow(/Invalid source_id/);
+    expect(() => normalizeAdminClientSourceScope('team-a', ['snake_case'], sources)).toThrow(/Invalid federated_read/);
+  });
+
+  test('rejects valid-looking but unregistered source ids', () => {
+    expect(() => normalizeAdminClientSourceScope('ghost', undefined, sources)).toThrow(/Unknown source_id/);
+    expect(() => normalizeAdminClientSourceScope('team-a', ['ghost'], sources)).toThrow(/Unknown federated_read/);
+  });
+});
@@ -78,6 +78,8 @@ describe('v0.36.1.x #1077 — admin register-client supports PKCE public clients
    // (under either name) from req.body. Pin the fallback pattern so the
    // PKCE-fix regression contract stays load-bearing.
    expect(src).toMatch(/req\.body[^;]*scopes\s*\?\?\s*[^;]*scope\b/);
+    expect(src).toMatch(/req\.body[^;]*source_id\s*\?\?\s*[^;]*sourceId\b/);
+    expect(src).toMatch(/req\.body[^;]*federated_read\s*\?\?\s*[^;]*federatedRead\b/);
    // v0.41.3 (T4 atomicity fix, codex F4): admin endpoint now validates
    // tokenEndpointAuthMethod via the shared validator and passes it to
    // registerClientManual as a positional arg. Pre-v0.41.3 the route did
@@ -87,6 +89,7 @@ describe('v0.36.1.x #1077 — admin register-client supports PKCE public clients
    // UPDATE block (the regex deliberately asserts the post-insert UPDATE
    // is GONE).
    expect(src).toMatch(/validateTokenEndpointAuthMethod\(tokenEndpointAuthMethod\)/);
+    expect(src).toMatch(/normalizeAdminClientSourceScope\(/);
    expect(src).toMatch(/registerClientManual\([^)]*validatedAuthMethod[^)]*\)/);
    // Regression guard: post-insert UPDATE flipping client_secret_hash to
    // NULL based on a runtime check is exactly the non-atomic pattern T4
@@ -267,3 +270,26 @@ describe('v0.42.43.0 #2095 — volunteer-events sink + cycle purge wiring (struc
    expect(src).toMatch(/purged_volunteer_events_count/);
  });
 });
+
+describe('#1490 + #1036 — admin Register Agent form exposes source scope + redirect URIs', () => {
+  test('Agents.tsx RegisterModal sends source_id + federated_read in the POST body (#1490)', () => {
+    const src = readFileSync('admin/src/pages/Agents.tsx', 'utf8');
+    expect(src).toMatch(/source_id:\s*sourceId/);
+    expect(src).toMatch(/federated_read:\s*federatedRead/);
+    // The source list comes from the requireAdmin-gated endpoint, not a hardcoded 'default'.
+    expect(src).toMatch(/api\.sources\(\)/);
+  });
+
+  test('serve-http.ts serves /admin/api/sources behind requireAdmin (#1490)', () => {
+    const src = readFileSync('src/commands/serve-http.ts', 'utf8');
+    expect(src).toMatch(/app\.get\('\/admin\/api\/sources',\s*requireAdmin/);
+  });
+
+  test('Agents.tsx RegisterModal sends redirectUris + authorization_code grants when URIs are entered (#1036)', () => {
+    const src = readFileSync('admin/src/pages/Agents.tsx', 'utf8');
+    // One-per-line textarea split into an array...
+    expect(src).toMatch(/redirectUris\.split\('\\n'\)/);
+    // ...included in the body with the CLI's grant-type inference convention.
+    expect(src).toMatch(/redirectUris:\s*uris,\s*grantTypes:\s*\['authorization_code',\s*'refresh_token'\]/);
+  });
+});
@@ -125,6 +125,30 @@ describe('client registration', () => {
    expect(client!.client_name).toBe('test-agent');
  });

+  test('registerClientManual persists source_id and federated_read into AuthInfo', async () => {
+    await sql`
+      INSERT INTO sources (id, name) VALUES (${'team-a'}, ${'Team A'}), (${'team-b'}, ${'Team B'})
+      ON CONFLICT DO NOTHING
+    `;
+    const { clientId, clientSecret } = await provider.registerClientManual(
+      'source-scoped-test',
+      ['client_credentials'],
+      'read write',
+      [],
+      'team-a',
+      ['team-a', 'team-b'],
+    );
+
+    const tokens = await provider.exchangeClientCredentials(clientId, clientSecret!, 'read');
+    const authInfo = await provider.verifyAccessToken(tokens.access_token) as {
+      sourceId?: string;
+      allowedSources?: string[];
+    };
+
+    expect(authInfo.sourceId).toBe('team-a');
+    expect(authInfo.allowedSources).toEqual(['team-a', 'team-b']);
+  });
+
  test('getClient returns undefined for unknown client', async () => {
    const client = await provider.clientsStore.getClient('nonexistent');
    expect(client).toBeUndefined();
@@ -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);
-  });
-});