fix(doctor): align maintenance scope with canonical files (#3854)

src/commands/doctor.ts

@@ -3742,7 +3742,9 @@ function collectMarkdownSlugs(root: string): Set<string> {
       continue;
     }
     for (const e of entries) {
-      if (e.name.startsWith('.') || e.name === 'node_modules') continue;
+      // Hidden directories can contain canonical, tracked knowledge (for
+      // example `.archive/`). Only implementation metadata is never a page.
+      if (e.name === '.git' || e.name === 'node_modules') continue;
       const childRel = rel ? `${rel}/${e.name}` : e.name;
       if (e.isDirectory()) stack.push(childRel);
       else if (/\.mdx?$/i.test(e.name)) out.add(slugifyPath(childRel).toLowerCase());

src/core/config.ts

@@ -1087,6 +1087,10 @@ export const KNOWN_CONFIG_KEYS: readonly string[] = [
   // consent reads this key, and enabling it is the documented path to
   // `gbrain takes extract --from-pages` — same unregistered-key class.
   'takes.bootstrap_enabled',
+  // Orphan reporting scope. These are consumed by core/orphan-policy.ts and
+  // documented there as the per-brain override path.
+  'orphans.exclude_prefixes',
+  'orphans.exclude_slugs',
   'sync.cost_gate_min_usd',
   'sync.federated_v2',
   'embed.backfill_cooldown_min',

test/config-set.test.ts

@@ -71,6 +71,11 @@ describe('KNOWN_CONFIG_KEYS', () => {
     expect(KNOWN_CONFIG_KEYS).not.toContain('conversation_parser.llm_polish_enabled');
   });
 
+  test('contains orphan-reporting override keys', () => {
+    expect(KNOWN_CONFIG_KEYS).toContain('orphans.exclude_prefixes');
+    expect(KNOWN_CONFIG_KEYS).toContain('orphans.exclude_slugs');
+  });
+
   test('no duplicate entries', () => {
     const set = new Set(KNOWN_CONFIG_KEYS);
     expect(set.size).toBe(KNOWN_CONFIG_KEYS.length);

test/doctor-silent-death-checks.test.ts

@@ -150,6 +150,16 @@ describe('undeclared_db_only_pages (#2784)', () => {
     expect(c.status).toBe('ok');
   });
 
+  test('file-backed page under a canonical hidden directory → ok', async () => {
+    const repo = makeRepo();
+    mkdirSync(join(repo, '.archive', 'people'), { recursive: true });
+    writeFileSync(join(repo, '.archive', 'people', 'alice-example.md'), '# Alice');
+    await addSource('src-a', repo);
+    await addPage('.archive/people/alice-example', { sourceId: 'src-a' });
+    const c = await checkUndeclaredDbOnlyPages(engine);
+    expect(c.status).toBe('ok');
+  });
+
   test('derive-phase default prefixes are implicitly declared', async () => {
     const repo = makeRepo();
     await addSource('src-a', repo);