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/core/ai/recipes/litellm-proxy.ts

@@ -56,36 +56,6 @@ export const litellmProxy: Recipe = {
       cost_per_1m_output_usd: undefined,
       price_last_verified: '2026-06-14',
     },
-    // LiteLLM normalizes Cohere / Voyage / Jina / etc. rerank backends to the
-    // same wire shape gbrain's gateway.rerank() already speaks (the
-    // ZeroEntropy/llama.cpp contract):
-    //   { model, query, documents, top_n } → { results: [{ index, relevance_score }] }
-    // So any rerank model the user registers in their LiteLLM config is
-    // reachable via `gbrain config set search.reranker.model litellm:<model>`
-    // with no request/response adapter — same as embeddings ride the proxy.
-    reranker: {
-      models: [], // user-provided; whatever rerank models the proxy serves
-      // No canonical default — the proxy defines its own model ids. The user
-      // sets search.reranker.model explicitly (mirrors the embedding
-      // touchpoint's user_provided_models contract).
-      default_model: '',
-      // The proxied backend bills (Cohere/Voyage/…); pricing-unknown is the
-      // honest state — same stance as this recipe's embedding/chat
-      // touchpoints and budget-tracker's deliberate litellm exclusion from
-      // the free-provider sets.
-      cost_per_1m_tokens_usd: undefined,
-      price_last_verified: '2026-06-27',
-      max_payload_bytes: 5_000_000,
-      // LEAF path only (matches llama-server-reranker's convention). LiteLLM
-      // serves both `/rerank` and `/v1/rerank`, and LITELLM_BASE_URL may be
-      // set with or without the `/v1` suffix (the setup_hint allows both), so
-      // the leaf form yields a valid route either way:
-      //   http://localhost:4000    + /rerank → /rerank        ✓
-      //   http://localhost:4000/v1 + /rerank → /v1/rerank     ✓
-      // Pinning '/v1/rerank' here would double to /v1/v1/rerank → 404 on
-      // /v1-suffixed bases.
-      path: '/rerank',
-    },
   },
-  setup_hint: 'Run LiteLLM (https://docs.litellm.ai) in front of any provider; set LITELLM_BASE_URL (include the /v1 suffix if your proxy serves the OpenAI route there, e.g. http://localhost:4000/v1) + pass --embedding-model litellm:<model> and --embedding-dimensions <N>. For rerank: register a rerank model in LiteLLM and set search.reranker.model litellm:<model-name>.',
+  setup_hint: 'Run LiteLLM (https://docs.litellm.ai) in front of any provider; set LITELLM_BASE_URL (include the /v1 suffix if your proxy serves the OpenAI route there, e.g. http://localhost:4000/v1) + pass --embedding-model litellm:<model> and --embedding-dimensions <N>.',
 };

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',
 ]);
 

test/ai/recipe-litellm-reranker.test.ts

@@ -1,88 +0,0 @@
-/**
- * litellm-proxy reranker touchpoint smoke.
- *
- * Sibling of recipe-llama-server-reranker.test.ts. Pins the reranker
- * touchpoint on the LiteLLM proxy recipe so:
- *  - the touchpoint exists with the LEAF '/rerank' path (LiteLLM serves both
- *    /rerank and /v1/rerank, so the leaf form is valid whether or not the
- *    user's LITELLM_BASE_URL carries the /v1 suffix the setup_hint allows)
- *  - a /v1-suffixed base URL does NOT produce /v1/v1/rerank (the original
- *    community PR pinned '/v1/rerank' which 404s on /v1-suffixed bases)
- *  - models: [] (user-provided; proxy defines the model ids)
- *  - pricing stays undefined (proxy can front a paid provider — same honest
- *    pricing-unknown stance as the embedding/chat touchpoints)
- *
- * The gateway.rerank() URL tests drive the real URL builder via the stubbed
- * transport (same seam as test/ai/rerank.test.ts).
- */
-
-import { describe, expect, test, afterEach } from 'bun:test';
-import { getRecipe } from '../../src/core/ai/recipes/index.ts';
-import {
-  configureGateway,
-  resetGateway,
-  rerank,
-  __setRerankTransportForTests,
-} from '../../src/core/ai/gateway.ts';
-
-afterEach(() => {
-  __setRerankTransportForTests(null);
-  resetGateway();
-});
-
-describe('recipe: litellm reranker touchpoint', () => {
-  test('declares reranker touchpoint with leaf /rerank path', () => {
-    const r = getRecipe('litellm')!;
-    const tp = r.touchpoints.reranker;
-    expect(tp).toBeDefined();
-    expect(tp!.path).toBe('/rerank');
-    expect(tp!.max_payload_bytes).toBe(5_000_000);
-  });
-
-  test('reranker touchpoint uses empty models[] for user-provided model ids', () => {
-    const r = getRecipe('litellm')!;
-    expect(r.touchpoints.reranker!.models).toEqual([]);
-  });
-
-  test('pricing stays undefined — proxy can front a paid provider', () => {
-    const r = getRecipe('litellm')!;
-    expect(r.touchpoints.reranker!.cost_per_1m_tokens_usd).toBeUndefined();
-  });
-
-  test('setup_hint keeps the /v1-suffix guidance AND mentions rerank', () => {
-    const r = getRecipe('litellm')!;
-    expect(r.setup_hint).toMatch(/\/v1 suffix/);
-    expect(r.setup_hint).toMatch(/search\.reranker\.model litellm:/);
-  });
-});
-
-describe('gateway.rerank() URL via litellm recipe', () => {
-  async function capturedRerankUrl(baseUrl?: string): Promise<string> {
-    configureGateway({
-      reranker_model: 'litellm:my-reranker',
-      env: {},
-      ...(baseUrl ? { base_urls: { litellm: baseUrl } } : {}),
-    });
-    let capturedUrl = '';
-    __setRerankTransportForTests(async (url) => {
-      capturedUrl = url;
-      return new Response(
-        JSON.stringify({ results: [{ index: 0, relevance_score: 0.9 }] }),
-        { status: 200, headers: { 'content-type': 'application/json' } },
-      );
-    });
-    await rerank({ query: 'q', documents: ['d'] });
-    return capturedUrl;
-  }
-
-  test('default base (no /v1 suffix) → /rerank', async () => {
-    const url = await capturedRerankUrl();
-    expect(url).toBe('http://localhost:4000/rerank');
-  });
-
-  test('/v1-suffixed base → /v1/rerank, NOT /v1/v1/rerank', async () => {
-    const url = await capturedRerankUrl('http://localhost:4000/v1');
-    expect(url).toBe('http://localhost:4000/v1/rerank');
-    expect(url).not.toContain('/v1/v1/');
-  });
-});

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[] = [];