fix(embed): extend #1717 model labeling to the embed-backfill stale path

src/core/embed-stale.ts (used by the embed-backfill minion handler) built
its merged ChunkInput without a model field, so every chunk on a touched
page — re-embedded AND preserved — was relabeled to the engine default on
each backfill pass. Mirror the embed.ts semantics: stamp the resolved
gateway label on re-embedded chunks, carry the existing label on untouched
ones. Pinned by a PGLite test that fails without the fix.

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

src/commands/embed.ts

@@ -1,5 +1,5 @@
 import type { BrainEngine } from '../core/engine.ts';
-import { embedBatch, currentEmbeddingSignature } from '../core/embedding.ts';
+import { embedBatch, currentEmbeddingSignature, resolveEmbeddingModelLabel } from '../core/embedding.ts';
 import type { ChunkInput } from '../core/types.ts';
 import { chunkText } from '../core/chunkers/recursive.ts';
 import { createProgress, type ProgressReporter } from '../core/progress.ts';
@@ -581,11 +581,16 @@ async function embedPage(
   for (let j = 0; j < toEmbed.length; j++) {
     embeddingMap.set(toEmbed[j].chunk_index, embeddings[j]);
   }
+  // #1717: label each (re)embedded chunk with the model that actually
+  // produced its vector. Preserved chunks (not re-embedded this pass) keep
+  // their existing model so a mixed-model page isn't relabeled wholesale.
+  const embedModelLabel = resolveEmbeddingModelLabel();
   const updated: ChunkInput[] = chunks.map(c => ({
     chunk_index: c.chunk_index,
     chunk_text: c.chunk_text,
     chunk_source: c.chunk_source,
     embedding: embeddingMap.get(c.chunk_index),
+    model: embeddingMap.has(c.chunk_index) && embedModelLabel ? embedModelLabel : c.model,
     token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
   }));
 
@@ -717,12 +722,16 @@ async function embedAll(
       for (let j = 0; j < toEmbed.length; j++) {
         embeddingMap.set(toEmbed[j].chunk_index, embeddings[j]);
       }
+      // #1717: stamp the resolved embedding model on (re)embedded chunks;
+      // preserve the existing model on chunks left untouched.
+      const embedModelLabel = resolveEmbeddingModelLabel();
       // Preserve ALL chunks, only update embeddings for stale ones
       const updated: ChunkInput[] = chunks.map(c => ({
         chunk_index: c.chunk_index,
         chunk_text: c.chunk_text,
         chunk_source: c.chunk_source,
         embedding: embeddingMap.get(c.chunk_index) ?? undefined,
+        model: embeddingMap.has(c.chunk_index) && embedModelLabel ? embedModelLabel : c.model,
         token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
       }));
       await observed(pacer, () => engine.upsertChunks(page.slug, updated, pageOpts));
@@ -1012,11 +1021,15 @@ async function embedAllStale(
           for (let j = 0; j < stale.length; j++) {
             staleIdxToEmbedding.set(stale[j].chunk_index, embeddings[j]);
           }
+          // #1717: label the re-embedded (stale) chunks with the resolved
+          // model; preserve the existing model on the non-stale chunks.
+          const embedModelLabel = resolveEmbeddingModelLabel();
           const merged: ChunkInput[] = existing.map(c => ({
             chunk_index: c.chunk_index,
             chunk_text: c.chunk_text,
             chunk_source: c.chunk_source,
             embedding: staleIdxToEmbedding.get(c.chunk_index) ?? undefined,
+            model: staleIdxToEmbedding.has(c.chunk_index) && embedModelLabel ? embedModelLabel : c.model,
             token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
           }));
           await observed(pacer, () => engine.upsertChunks(slug, merged, { sourceId: keySourceId }));

src/core/doctor-categories.ts

@@ -35,11 +35,10 @@
  *
  * The doctor renders both side by side.
  *
- * Drift contract: every check name that ships through doctor MUST appear in
+ * Drift contract: every check name that ships in doctor.ts MUST appear in
  * exactly one set below. The drift-guard test in
- * `test/doctor-categories.test.ts` enforces this by reading doctor check
- * emitter sources via a tagged-string scan and asserting set membership
- * exactly.
+ * `test/doctor-categories.test.ts` enforces this by reading doctor.ts source
+ * 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
@@ -68,15 +67,12 @@ 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',
@@ -106,9 +102,7 @@ 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',
 ]);
@@ -176,14 +170,12 @@ 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/embed-stale.ts

@@ -20,6 +20,7 @@
 import type { BrainEngine } from './engine.ts';
 import type { ChunkInput } from './types.ts';
 import { embedBatchWithBackoff } from '../commands/embed.ts';
+import { resolveEmbeddingModelLabel } from './embedding.ts';
 import { type DbPacer, createNoopPacer, observed } from './db-pacer.ts';
 import { AbortError } from './abort-check.ts';
 
@@ -200,11 +201,17 @@ export async function embedStaleForSource(
         for (let j = 0; j < stale.length; j++) {
           staleIdxToEmbedding.set(stale[j].chunk_index, embeddings[j]);
         }
+        // #1717: label re-embedded chunks with the model that produced the
+        // vector; preserved chunks keep their existing model. Without this,
+        // upsertChunks falls back to DEFAULT_EMBEDDING_MODEL for every chunk
+        // (the same mislabel the embed.ts paths fixed).
+        const embedModelLabel = resolveEmbeddingModelLabel();
         const merged: ChunkInput[] = existing.map((c) => ({
           chunk_index: c.chunk_index,
           chunk_text: c.chunk_text,
           chunk_source: c.chunk_source,
           embedding: staleIdxToEmbedding.get(c.chunk_index) ?? undefined,
+          model: staleIdxToEmbedding.has(c.chunk_index) && embedModelLabel ? embedModelLabel : c.model,
           token_count: c.token_count || Math.ceil(c.chunk_text.length / 4),
           // Carry through per-chunk metadata. upsertChunks writes these as
           // EXCLUDED.<col> (not COALESCE), so omitting them here resets image

src/core/embedding.ts

@@ -113,6 +113,21 @@ export async function embedBatch(
   return results;
 }
 
+/**
+ * Resolve the embedding model label (`provider:model`) to stamp onto
+ * `content_chunks.model`, so each chunk records the model that actually
+ * produced its vector instead of the engine's hardcoded default (#1717).
+ * Returns undefined if the gateway is unconfigured; callers then fall back
+ * to the chunk's existing model rather than mislabeling it.
+ */
+export function resolveEmbeddingModelLabel(): string | undefined {
+  try {
+    return gatewayGetModel();
+  } catch {
+    return undefined;
+  }
+}
+
 /** Currently-configured embedding model (short form without provider prefix). */
 export function getEmbeddingModelName(): string {
   return gatewayGetModel().split(':').slice(1).join(':') || 'text-embedding-3-large';

src/core/import-file.ts

@@ -8,7 +8,7 @@ import { chunkText } from './chunkers/recursive.ts';
 import { chunkCodeText, chunkCodeTextFull, detectCodeLanguage, CHUNKER_VERSION } from './chunkers/code.ts';
 import { findChunkForOffset } from './chunkers/edge-extractor.ts';
 import { extractCodeRefs, imageOfCandidates } from './link-extraction.ts';
-import { embedBatch, embedMultimodal, currentEmbeddingSignature } from './embedding.ts';
+import { embedBatch, embedMultimodal, currentEmbeddingSignature, resolveEmbeddingModelLabel } from './embedding.ts';
 import { slugifyPath, slugifyCodePath, isCodeFilePath } from './sync.ts';
 import type { ChunkInput, PageInput, PageType } from './types.ts';
 import { computeEffectiveDate } from './effective-date.ts';
@@ -716,8 +716,12 @@ export async function importFromContent(
       ? chunks.map((c) => wrapChunkForEmbedding(c.chunk_text, prefix, c.chunk_source))
       : chunks.map((c) => c.chunk_text);
     const embeddings = await embedBatch(wrappedTexts);
+    // #1717: label each chunk with the model that actually produced its
+    // vector, not the engine's hardcoded default.
+    const embedModelLabel = resolveEmbeddingModelLabel();
     for (let i = 0; i < chunks.length; i++) {
       chunks[i].embedding = embeddings[i];
+      if (embedModelLabel) chunks[i].model = embedModelLabel;
       // token_count tracks the wrapped string length so cost reporting
       // reflects what we actually sent to the embedder.
       chunks[i].token_count = Math.ceil(wrappedTexts[i].length / 4);
@@ -1141,7 +1145,10 @@ export async function importCodeFile(
     const matched = existingByKey.get(key);
     if (matched && matched.embedding) {
       // Reuse the existing embedding verbatim. No API call, no cost.
+      // #1717: carry the existing model label along with the reused vector
+      // so the upsert doesn't relabel it with the engine default.
       chunks[i]!.embedding = matched.embedding as Float32Array;
+      chunks[i]!.model = matched.model ?? undefined;
       chunks[i]!.token_count = matched.token_count ?? undefined;
     } else {
       needsEmbedIndexes.push(i);
@@ -1153,9 +1160,12 @@ export async function importCodeFile(
     try {
       const textsToEmbed = needsEmbedIndexes.map((i) => chunks[i]!.chunk_text);
       const embeddings = await embedBatch(textsToEmbed);
+      // #1717: stamp the model that produced these vectors.
+      const embedModelLabel = resolveEmbeddingModelLabel();
       for (let j = 0; j < needsEmbedIndexes.length; j++) {
         const i = needsEmbedIndexes[j]!;
         chunks[i]!.embedding = embeddings[j]!;
+        if (embedModelLabel) chunks[i]!.model = embedModelLabel;
         chunks[i]!.token_count = Math.ceil(chunks[i]!.chunk_text.length / 4);
       }
     } catch (e: unknown) {

test/doctor-categories.test.ts

@@ -1,10 +1,10 @@
 /**
  * Drift guard for src/core/doctor-categories.ts.
  *
- * 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.
+ * 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.
  *
  * This is the structural failure the v0.41.19.0 plan-eng-review caught:
  * doctor.ts grows new checks regularly; without this guard, the
@@ -25,30 +25,26 @@ 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>();
-  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]);
-    }
+  // 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 doctor-emitted check name belongs to exactly one category set', () => {
+  test('every check name in doctor.ts source belongs to exactly one category set', () => {
     const discovered = enumerateCheckNames();
     const allCategorized = new Set<string>([
       ...BRAIN_CHECK_NAMES,
@@ -63,7 +59,7 @@ describe('doctor-categories drift guard', () => {
     }
     if (missing.length > 0) {
       throw new Error(
-        `These check names appear in doctor check emitters but are not categorized in ` +
+        `These check names appear in doctor.ts but are not categorized in ` +
           `src/core/doctor-categories.ts: ${missing.sort().join(', ')}. ` +
           `Add each to BRAIN/SKILL/OPS/META_CHECK_NAMES.`,
       );
@@ -90,7 +86,7 @@ describe('doctor-categories drift guard', () => {
     expect(dupes).toEqual([]);
   });
 
-  test('every categorized name is currently used in doctor check emitters (no stale entries)', () => {
+  test('every categorized name is currently used in doctor.ts source (no stale entries)', () => {
     const discovered = enumerateCheckNames();
     const allCategorized = new Set<string>([
       ...BRAIN_CHECK_NAMES,
@@ -128,14 +124,6 @@ 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');
@@ -152,24 +140,6 @@ 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/embed-stale.serial.test.ts

@@ -15,6 +15,7 @@ import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:tes
 import { PGLiteEngine } from '../src/core/pglite-engine.ts';
 import { resetPgliteState } from './helpers/reset-pglite.ts';
 import { embedStaleForSource } from '../src/core/embed-stale.ts';
+import { configureGateway, resetGateway } from '../src/core/ai/gateway.ts';
 import type { ChunkInput } from '../src/core/types.ts';
 
 let engine: PGLiteEngine;
@@ -276,4 +277,49 @@ describe('embedStaleForSource', () => {
     // The stale text row actually got its embedding.
     expect(txtRow.embedded_at).not.toBeNull();
   });
+
+  // #1717: the backfill path must label re-embedded chunks with the model
+  // that produced the vector, and preserve the existing label on chunks it
+  // did not touch (before the fix, both were reset to the engine default).
+  test('labels re-embedded chunks with the gateway model, preserves untouched labels (#1717)', async () => {
+    configureGateway({
+      embedding_model: 'openai:text-embedding-3-large',
+      env: { OPENAI_API_KEY: 'sk-test-embed-stale-1717' },
+    });
+    try {
+      await engine.putPage('notes/model-label', {
+        type: 'note',
+        title: 'model-label',
+        compiled_truth: '# model-label\n\nseeded',
+      });
+      await engine.upsertChunks('notes/model-label', [
+        {
+          chunk_index: 0,
+          chunk_text: 'already embedded elsewhere',
+          chunk_source: 'compiled_truth',
+          embedding: new Float32Array(1536).fill(0.01),
+          model: 'voyage:voyage-3',
+          token_count: 4,
+        },
+        {
+          chunk_index: 1,
+          chunk_text: 'stale chunk needing embed',
+          chunk_source: 'compiled_truth',
+          token_count: 5,
+          embedding: undefined, // stale
+        },
+      ]);
+
+      const result = await embedStaleForSource(engine, 'default', { embedFn: fakeEmbedFn });
+      expect(result.embedded).toBe(1);
+
+      const after = await engine.getChunks('notes/model-label');
+      const preserved = after.find((c) => c.chunk_index === 0)!;
+      const reembedded = after.find((c) => c.chunk_index === 1)!;
+      expect(reembedded.model).toBe('openai:text-embedding-3-large');
+      expect(preserved.model).toBe('voyage:voyage-3');
+    } finally {
+      resetGateway();
+    }
+  });
 });

test/embed.serial.test.ts

@@ -37,6 +37,8 @@ mock.module('../src/core/embedding.ts', () => ({
   // setPageEmbeddingSignature / invalidateStaleSignatureEmbeddings resolve to
   // null via the Proxy default, so the signature value is inert here.
   currentEmbeddingSignature: () => 'test:model:1536',
+  // #1717: embed paths stamp this label on (re)embedded chunks.
+  resolveEmbeddingModelLabel: () => 'openai:text-embedding-3-large',
 }));
 
 // Import AFTER mocking.
@@ -803,3 +805,34 @@ describe('embedAllStale --source threading (D7)', () => {
     expect((firstCallOpts as { sourceId?: string }).sourceId).toBe('media-corpus');
   });
 });
+
+// #1717: content_chunks.model must record the model that actually produced
+// each vector, not the gateway/engine default.
+describe('content_chunks.model labeling (#1717)', () => {
+  test('stamps the resolved embedding model on re-embedded chunks, preserves it on untouched chunks', async () => {
+    let upserted: any[] | undefined;
+    // Chunk 0 is stale (no embedded_at) → gets re-embedded this pass.
+    // Chunk 1 is already embedded with a DIFFERENT model → must be preserved,
+    // not relabeled to the current model.
+    const chunks = [
+      { chunk_index: 0, chunk_text: 'a', chunk_source: 'compiled_truth', embedded_at: null, model: 'zeroentropyai:zembed-1', token_count: 1 },
+      { chunk_index: 1, chunk_text: 'b', chunk_source: 'compiled_truth', embedded_at: '2026-01-01', embedding: new Float32Array(1536), model: 'voyage:voyage-3', token_count: 1 },
+    ];
+    const engine = mockEngine({
+      getPage: async () => ({ slug: 'notes/x', compiled_truth: 'a', timeline: '', source_id: 'default' }),
+      getChunks: async () => chunks,
+      upsertChunks: async (_slug: string, c: any[]) => { upserted = c; },
+      setPageEmbeddingSignature: async () => null,
+    });
+
+    await runEmbedCore(engine, { slugs: ['notes/x'] });
+
+    expect(upserted).toBeDefined();
+    const byIdx = Object.fromEntries(upserted!.map(c => [c.chunk_index, c]));
+    // Re-embedded chunk carries the model that produced its vector (was
+    // mislabeled with the default before the fix).
+    expect(byIdx[0].model).toBe('openai:text-embedding-3-large');
+    // Untouched chunk keeps its original model — no wholesale relabel.
+    expect(byIdx[1].model).toBe('voyage:voyage-3');
+  });
+});

test/import-signature-stamp.serial.test.ts

@@ -73,4 +73,21 @@ describe('importFromContent embedding_signature stamping (F1)', () => {
     await importFromContent(engine, 'concepts/unstamped', '# Unstamped\n\nbody content.', { noEmbed: true });
     expect(await signatureOf('concepts/unstamped')).toBeNull();
   });
+
+  // #1717: content_chunks.model must record the model that produced the
+  // vector (the configured gateway model), not the engine's hardcoded
+  // default. The gateway here is configured to openai:text-embedding-3-large,
+  // which differs from DEFAULT_EMBEDDING_MODEL — so this fails without the
+  // import-path model stamping.
+  test('inline embed labels content_chunks.model with the configured model (#1717)', async () => {
+    await importFromContent(engine, 'concepts/labeled', '# Labeled\n\nsome body content to chunk and embed.', {});
+    const rows = await engine.executeRaw<{ model: string }>(
+      `SELECT cc.model FROM content_chunks cc
+        JOIN pages p ON p.id = cc.page_id
+       WHERE p.slug = $1 AND p.source_id = 'default'`,
+      ['concepts/labeled'],
+    );
+    expect(rows.length).toBeGreaterThan(0);
+    for (const r of rows) expect(r.model).toBe('openai:text-embedding-3-large');
+  });
 });