fix(doctor): register onboard check names in doctor-categories to stop unknown-check warnings

doctor.ts pushes runAllOnboardChecks results into the checks list, but the
7 onboard check names (embed_staleness, entity_link_coverage,
timeline_coverage, takes_count, dangling_aliases, pack_upgrade_available,
type_proliferation) were never added to doctor-categories.ts, so every
doctor run emitted an 'unknown check name' stderr warn per onboard check.

Registers the 5 data-quality names under BRAIN and the 2 schema-pack names
under META (alphabetical order preserved), and widens the drift-guard test
to scan src/core/onboard/checks.ts alongside src/commands/doctor.ts so
future onboard checks can't drift uncategorized.

Takeover of #1839, rebased onto master (keeps master's timeline_dedup_index).

Co-authored-by: mvanhorn <mvanhorn@users.noreply.github.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

src/commands/extract.ts

@@ -43,7 +43,7 @@ import {
 } from '../core/link-extraction.ts';
 import { createProgress } from '../core/progress.ts';
 import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts';
-import { pathToSlug, slugifyPath, pruneDir, isSyncable } from '../core/sync.ts';
+import { pathToSlug, pruneDir, isSyncable } from '../core/sync.ts';
 // v0.41.18.0: withRetry + isRetryableConnError + WithRetryOpts moved to
 // src/core/retry.ts as the canonical primitive. Engine methods
 // (addLinksBatch/addTimelineEntriesBatch/upsertChunks) now self-retry via
@@ -269,24 +269,14 @@ export function extractMarkdownLinks(content: string): { name: string; relTarget
 export function resolveSlug(fileDir: string, relTarget: string, allSlugs: Set<string>): string | null {
   const targetNoExt = relTarget.endsWith('.md') ? relTarget.slice(0, -3) : relTarget;
 
-  // Issue #1964: wikilinks carry raw Obsidian paths (`[[llm-wiki/entities/AI 3.0]]`)
-  // but allSlugs holds sync-slugified slugs (`llm-wiki/entities/ai-3.0`). Try the
-  // raw candidate first (back-compat), then the sync-consistent slugified form.
-  const hit = (candidate: string): string | null => {
-    if (allSlugs.has(candidate)) return candidate;
-    const slugified = slugifyPath(candidate);
-    if (slugified !== candidate && allSlugs.has(slugified)) return slugified;
-    return null;
-  };
-
-  const s1 = hit(join(fileDir, targetNoExt));
-  if (s1) return s1;
+  const s1 = join(fileDir, targetNoExt);
+  if (allSlugs.has(s1)) return s1;
 
   const parts = fileDir.split('/').filter(Boolean);
   for (let strip = 1; strip <= parts.length; strip++) {
     const ancestor = parts.slice(0, parts.length - strip).join('/');
-    const candidate = hit(ancestor ? join(ancestor, targetNoExt) : targetNoExt);
-    if (candidate) return candidate;
+    const candidate = ancestor ? join(ancestor, targetNoExt) : targetNoExt;
+    if (allSlugs.has(candidate)) return candidate;
   }
 
   return null;

src/core/doctor-categories.ts

@@ -35,10 +35,11 @@
  *
  * The doctor renders both side by side.
  *
- * Drift contract: every check name that ships in doctor.ts MUST appear in
+ * Drift contract: every check name that ships through doctor MUST appear in
  * exactly one set below. The drift-guard test in
- * `test/doctor-categories.test.ts` enforces this by reading doctor.ts source
- * via a tagged-string scan and asserting set membership exactly.
+ * `test/doctor-categories.test.ts` enforces this by reading doctor check
+ * emitter sources via a tagged-string scan and asserting set membership
+ * exactly.
  *
  * If you add a new doctor check, you MUST add its name to the appropriate
  * set here. The categorize step in `src/commands/doctor.ts` falls through
@@ -67,12 +68,15 @@ export const BRAIN_CHECK_NAMES: ReadonlySet<string> = new Set([
   'conversation_parser_probe_health',
   'cross_modal_modality_backfill',
   'cycle_freshness',
+  'dangling_aliases',
   'effective_date_health',
+  'embed_staleness',
   'embedding_column_registry',
   'embedding_env_override',
   'embedding_provider',
   'embedding_width_consistency',
   'embeddings',
+  'entity_link_coverage',
   'eval_drift',
   'extract_atoms_backlog',
   'extract_health',
@@ -102,7 +106,9 @@ export const BRAIN_CHECK_NAMES: ReadonlySet<string> = new Set([
   'stub_guard_24h',
   'sync_failures',
   'sync_freshness',
+  'takes_count',
   'takes_weight_grid',
+  'timeline_coverage',
   'unified_multimodal_coverage',
   'voice_gate_health',
 ]);
@@ -170,12 +176,14 @@ export const META_CHECK_NAMES: ReadonlySet<string> = new Set([
   'eval_capture',
   'minions_migration',
   'multi_source_drift',
+  'pack_upgrade_available',
   'schema_pack_active',
   'schema_pack_consistency',
   'schema_pack_source_drift',
   'schema_version',
   'slug_fallback_audit',
   'timeline_dedup_index',
+  'type_proliferation',
   'upgrade_errors',
 ]);
 

src/core/link-extraction.ts

@@ -14,7 +14,6 @@
 import type { BrainEngine } from './engine.ts';
 import type { PageType } from './types.ts';
 import { ensureWellFormed } from './text-safe.ts';
-import { slugifyPath } from './sync.ts';
 
 /**
  * v0.42.7 — link-extraction version stamp. Bump this ISO timestamp whenever the
@@ -483,29 +482,14 @@ export async function extractPageLinks(
     // pre-v0.40.8.2 behavior of dropping bare wikilinks outside
     // DIR_PATTERN.
     if (ref.needsResolution) {
-      if (typeof resolver.resolveBasenameMatches !== 'function') continue;
+      if (!opts.globalBasename || typeof resolver.resolveBasenameMatches !== 'function') {
+        continue;
+      }
       // Issue #972 (codex): resolve by the wikilink TARGET (ref.slug — the
       // text inside `[[...]]` before any `|`), NOT the display alias
       // (ref.name = match[2]). `[[struktura|the project]]` must resolve
       // `struktura`, not "the project". The display text is for context only.
-      //
-      // Issue #1964: a dir-qualified wikilink (`[[llm-wiki/entities/AI 3.0]]`)
-      // carries a raw Obsidian path while page slugs are sync-slugified
-      // (`llm-wiki/entities/ai-3.0`). Slugify the path the same way sync does,
-      // then match by exact slug or path-suffix (wiki-root-relative authoring).
-      // This runs regardless of global_basename — it's dir-qualified, so the
-      // cross-dir false-positive risk the flag guards against doesn't apply.
-      // Mirrors the FS path's resolveSlug ancestor walk. Bare `[[name]]`
-      // wikilinks still require the global_basename flag.
-      let matches: string[] = [];
-      const slugified = ref.slug.includes('/') ? slugifyPath(ref.slug) : '';
-      if (slugified.includes('/')) {
-        const tail = slugified.slice(slugified.lastIndexOf('/') + 1);
-        matches = (await resolver.resolveBasenameMatches(tail))
-          .filter(m => m === slugified || m.endsWith(`/${slugified}`));
-      } else if (opts.globalBasename) {
-        matches = await resolver.resolveBasenameMatches(ref.slug);
-      }
+      const matches = await resolver.resolveBasenameMatches(ref.slug);
       if (matches.length === 0) continue;
       const idx = content.indexOf(ref.slug);
       const context = idx >= 0 ? excerpt(content, idx, 240) : ref.name;

test/doctor-categories.test.ts

@@ -1,10 +1,10 @@
 /**
  * Drift guard for src/core/doctor-categories.ts.
  *
- * Reads src/commands/doctor.ts source via a literal-string scan, enumerates
- * every `name: '<...>'` Check name, and asserts each appears in exactly ONE
- * category set. The union of the four sets must equal the discovered names
- * exactly — no orphans, no extras.
+ * Reads doctor check emitter source via a literal-string scan, enumerates every
+ * `name: '<...>'` Check name, and asserts each appears in exactly ONE category
+ * set. The union of the four sets must equal the discovered names exactly —
+ * no orphans, no extras.
  *
  * This is the structural failure the v0.41.19.0 plan-eng-review caught:
  * doctor.ts grows new checks regularly; without this guard, the
@@ -25,26 +25,30 @@ import {
 } from '../src/core/doctor-categories.ts';
 
 const DOCTOR_TS_PATH = join(import.meta.dir, '..', 'src', 'commands', 'doctor.ts');
+const ONBOARD_CHECKS_TS_PATH = join(import.meta.dir, '..', 'src', 'core', 'onboard', 'checks.ts');
+const CHECK_SOURCE_PATHS = [DOCTOR_TS_PATH, ONBOARD_CHECKS_TS_PATH];
 
 function enumerateCheckNames(): Set<string> {
-  const source = readFileSync(DOCTOR_TS_PATH, 'utf-8');
   const names = new Set<string>();
-  // 1) Inline object-literal form: `{ name: 'foo', ... }`.
-  for (const m of source.matchAll(/name:\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
-    names.add(m[1]);
-  }
-  // 2) Helper-function form: `const name = 'foo';` inside a check helper.
-  //    Catches checks like `nightly_quality_probe_health` and
-  //    `conversation_facts_backlog` that build the Check from a captured
-  //    name constant.
-  for (const m of source.matchAll(/const\s+name\s*=\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
-    names.add(m[1]);
+  for (const path of CHECK_SOURCE_PATHS) {
+    const source = readFileSync(path, 'utf-8');
+    // 1) Inline object-literal form: `{ name: 'foo', ... }`.
+    for (const m of source.matchAll(/name:\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
+      names.add(m[1]);
+    }
+    // 2) Helper-function form: `const name = 'foo';` inside a check helper.
+    //    Catches checks like `nightly_quality_probe_health` and
+    //    `conversation_facts_backlog` that build the Check from a captured
+    //    name constant.
+    for (const m of source.matchAll(/const\s+name\s*=\s*['"]([a-z][a-z0-9_]+)['"]/g)) {
+      names.add(m[1]);
+    }
   }
   return names;
 }
 
 describe('doctor-categories drift guard', () => {
-  test('every check name in doctor.ts source belongs to exactly one category set', () => {
+  test('every doctor-emitted check name belongs to exactly one category set', () => {
     const discovered = enumerateCheckNames();
     const allCategorized = new Set<string>([
       ...BRAIN_CHECK_NAMES,
@@ -59,7 +63,7 @@ describe('doctor-categories drift guard', () => {
     }
     if (missing.length > 0) {
       throw new Error(
-        `These check names appear in doctor.ts but are not categorized in ` +
+        `These check names appear in doctor check emitters but are not categorized in ` +
           `src/core/doctor-categories.ts: ${missing.sort().join(', ')}. ` +
           `Add each to BRAIN/SKILL/OPS/META_CHECK_NAMES.`,
       );
@@ -86,7 +90,7 @@ describe('doctor-categories drift guard', () => {
     expect(dupes).toEqual([]);
   });
 
-  test('every categorized name is currently used in doctor.ts source (no stale entries)', () => {
+  test('every categorized name is currently used in doctor check emitters (no stale entries)', () => {
     const discovered = enumerateCheckNames();
     const allCategorized = new Set<string>([
       ...BRAIN_CHECK_NAMES,
@@ -124,6 +128,14 @@ describe('categorizeCheck', () => {
     expect(categorizeCheck('sync_freshness')).toBe('brain');
   });
 
+  test('returns the right category for onboard data-quality check names', () => {
+    expect(categorizeCheck('embed_staleness')).toBe('brain');
+    expect(categorizeCheck('entity_link_coverage')).toBe('brain');
+    expect(categorizeCheck('timeline_coverage')).toBe('brain');
+    expect(categorizeCheck('takes_count')).toBe('brain');
+    expect(categorizeCheck('dangling_aliases')).toBe('brain');
+  });
+
   test('returns the right category for a known skill name', () => {
     expect(categorizeCheck('resolver_health')).toBe('skill');
     expect(categorizeCheck('skill_conformance')).toBe('skill');
@@ -140,6 +152,24 @@ describe('categorizeCheck', () => {
     expect(categorizeCheck('upgrade_errors')).toBe('meta');
   });
 
+  test('returns the right category for onboard schema-pack check names without warning', () => {
+    const originalWrite = process.stderr.write.bind(process.stderr);
+    const captured: string[] = [];
+    (process.stderr as { write: typeof process.stderr.write }).write = ((
+      chunk: string | Uint8Array,
+    ) => {
+      captured.push(typeof chunk === 'string' ? chunk : Buffer.from(chunk).toString());
+      return true;
+    }) as typeof process.stderr.write;
+    try {
+      expect(categorizeCheck('pack_upgrade_available')).toBe('meta');
+      expect(categorizeCheck('type_proliferation')).toBe('meta');
+      expect(captured.filter((c) => c.includes('[doctor-categories]'))).toEqual([]);
+    } finally {
+      (process.stderr as { write: typeof process.stderr.write }).write = originalWrite;
+    }
+  });
+
   test('unknown check name falls through to meta with a stderr warn (once per process)', () => {
     const originalWrite = process.stderr.write.bind(process.stderr);
     const captured: string[] = [];

test/extract-fs.test.ts

@@ -389,33 +389,6 @@ describe('resolveSlugAll', () => {
   });
 });
 
-// ─── issue #1964: cross-directory wikilinks — slug/path mismatch ──────────
-
-describe('issue #1964: raw Obsidian wikilink paths resolve to sync-slugified slugs', () => {
-  test('resolveSlug slugifies the candidate (sync-consistent), no flag needed', () => {
-    const all = new Set(['llm-wiki/entities/ai-3.0']);
-    // Wikilink literal `[[llm-wiki/entities/AI 3.0]]` — spaces + uppercase.
-    expect(resolveSlug('llm-wiki/notes', 'llm-wiki/entities/AI 3.0.md', all))
-      .toBe('llm-wiki/entities/ai-3.0');
-  });
-
-  test('resolveSlug slugifies raw (unslugified) fileDir too', () => {
-    const all = new Set(['llm-wiki/entities/ai-3.0']);
-    // fileDir comes from dirname(relPath) — the raw on-disk directory.
-    expect(resolveSlug('LLM Wiki/Notes', 'entities/AI 3.0.md', all))
-      .toBe('llm-wiki/entities/ai-3.0');
-  });
-
-  test('extractLinksFromFile resolves cross-directory wikilink with flag OFF as a typed edge', async () => {
-    const allSlugs = new Set(['llm-wiki/entities/ai-3.0', 'llm-wiki/notes/roadmap']);
-    const content = '---\ntitle: Roadmap\ntype: concept\n---\n\nSee [[llm-wiki/entities/AI 3.0]].\n';
-    const links = await extractLinksFromFile(content, 'llm-wiki/notes/roadmap.md', allSlugs);
-    expect(links.map(l => l.to_slug)).toEqual(['llm-wiki/entities/ai-3.0']);
-    // Dir-qualified path resolution is exact, NOT the basename fallback.
-    expect(links[0].link_type).not.toBe('wikilink_basename');
-  });
-});
-
 describe('issue #972 repro: bare wikilinks resolve when flag is on', () => {
   // End-to-end: reproduces the issue's exact repro inside a tempdir +
   // PGLite, then asserts edge count under both flag states.

test/link-extraction.test.ts

@@ -9,8 +9,6 @@ import {
   parseTimelineEntries,
   isAutoLinkEnabled,
   FRONTMATTER_LINK_MAP,
-  buildBasenameIndex,
-  queryBasenameIndex,
   type SlugResolver,
 } from '../src/core/link-extraction.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
@@ -426,46 +424,6 @@ describe('extractPageLinks', () => {
     expect(strk!.linkType).toBe('wikilink_basename');
   });
 
-  // ─── issue #1964: dir-qualified wikilinks with raw Obsidian paths ────────
-
-  test('#1964: dir-qualified wikilink resolves via sync-consistent slugification (flag OFF)', async () => {
-    // `[[llm-wiki/entities/AI 3.0]]` is a raw Obsidian path; the page slug
-    // is the sync-slugified `llm-wiki/entities/ai-3.0`. Must resolve WITHOUT
-    // global_basename (it's dir-qualified) and must NOT leak to a same-tail
-    // page in a different directory.
-    const resolver: SlugResolver = {
-      resolve: async () => null,
-      resolveBasenameMatches: async (name) =>
-        name === 'ai-3.0' ? ['other/ai-3.0', 'llm-wiki/entities/ai-3.0'] : [],
-    };
-    const { candidates } = await extractPageLinks(
-      'llm-wiki/notes/roadmap',
-      'See [[llm-wiki/entities/AI 3.0]] for the model.',
-      {}, 'concept', resolver,
-      // opts.globalBasename omitted (= false) — path is dir-qualified
-    );
-    expect(candidates.map(c => c.targetSlug)).toEqual(['llm-wiki/entities/ai-3.0']);
-    expect(candidates[0].linkType).toBe('wikilink_basename');
-    expect(candidates[0].linkSource).toBe('wikilink-resolved');
-  });
-
-  test('#1964: path-suffix match resolves wiki-root-relative paths against a real index', async () => {
-    // Author writes `[[llm-wiki/entities/AI 3.0]]` but the brain nests the
-    // wiki under a vault dir. Suffix match rescues it; queried through the
-    // REAL basename index so the tail-key lookup is exercised end to end.
-    const idx = buildBasenameIndex(['vault/llm-wiki/entities/ai-3.0', 'people/ai-3.0']);
-    const resolver: SlugResolver = {
-      resolve: async () => null,
-      resolveBasenameMatches: async (name) => queryBasenameIndex(idx, name),
-    };
-    const { candidates } = await extractPageLinks(
-      'vault/llm-wiki/notes/roadmap',
-      'See [[llm-wiki/entities/AI 3.0]].',
-      {}, 'concept', resolver,
-    );
-    expect(candidates.map(c => c.targetSlug)).toEqual(['vault/llm-wiki/entities/ai-3.0']);
-  });
-
   test('opts.skipFrontmatter suppresses the frontmatter pass', async () => {
     // Real resolver shape that WOULD resolve frontmatter source: too,
     // but skipFrontmatter blocks the path entirely.