fix(dream): stamp incremental extraction watermark (#2636)

The Dream cycle disables sync's inline extraction and routes changed
slugs through extractForSlugs, which flushed link/timeline batches but
never stamped links_extracted_at — so incrementally extracted pages
stayed permanently visible to `extract --stale` / doctor.

Collect processedRefs per successfully processed page and stamp them
via stampExtracted (best-effort) after both batch flushes, non-dry-run
mode 'all' only. Source-id threading from the original PR #2637 already
landed on master via #1503/#1747, so this rebase carries only the
missing watermark stamp plus regression tests.

Takeover of #2637.

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

src/commands/extract.ts

@@ -1025,6 +1025,10 @@ async function extractForSlugs(
   let linksCreated = 0;
   let timelineCreated = 0;
   let pagesProcessed = 0;
+  // #2636: successfully processed pages get their extraction watermark
+  // stamped after the final flush (mode 'all' only — a partial-mode run
+  // hasn't done the full extraction the watermark asserts).
+  const processedRefs: Array<{ slug: string; source_id: string }> = [];
 
   // Issue #972: read the basename flag once per extract run.
   const globalBasename = await isGlobalBasenameEnabled(engine);
@@ -1113,6 +1117,7 @@ async function extractForSlugs(
         }
 
         pagesProcessed++;
+        if (!dryRun) processedRefs.push({ slug, source_id: sourceId ?? 'default' });
       } catch { /* skip unreadable */ }
       progress.tick(1);
     },
@@ -1120,6 +1125,13 @@ async function extractForSlugs(
 
   await flushLinks();
   await flushTimeline();
+  // #2636: the Dream cycle disables sync's inline extraction and routes
+  // changed slugs through this incremental path — without a stamp here,
+  // those pages never get links_extracted_at and stay permanently visible
+  // to `extract --stale` / doctor. Stamp only after BOTH batches flushed.
+  if (!dryRun && mode === 'all') {
+    await stampExtracted(engine, processedRefs);
+  }
   progress.finish();
 
   if (!jsonMode) {

src/core/import-file.ts

@@ -36,7 +36,7 @@ import {
 } from './embedding-context.ts';
 import { loadSearchModeConfig, resolveSearchMode } from './search/mode.ts';
 import { normalizeAliasList } from './search/alias-normalize.ts';
-import { isUndefinedTableError, warnOncePerProcess, validateSlug } from './utils.ts';
+import { isUndefinedTableError, warnOncePerProcess } from './utils.ts';
 import { computeCorpusGeneration } from './contextual-retrieval-service.ts';
 import { runGuardrails } from './guardrails.ts';
 
@@ -295,12 +295,6 @@ export async function importFromContent(
     remote?: boolean;
   } = {},
 ): Promise<ImportResult> {
-  // Normalize BEFORE any tx write: putPage lowercases via validateSlug but
-  // upsertChunks used to query by the caller's raw slug, so a mixed-case slug
-  // created the page row then failed the chunk upsert with "Page not found",
-  // rolling back the whole import (#430).
-  slug = validateSlug(slug);
-
   // v0.18.0+ multi-source: when caller is syncing under a non-default source,
   // every per-page tx call must carry `sourceId` so writes target the right
   // (source_id, slug) row. Pre-fix, putPage relied on the schema DEFAULT and

src/core/pglite-engine.ts

@@ -2235,9 +2235,6 @@ export class PGLiteEngine implements BrainEngine {
   }
 
   private async _upsertChunksOnce(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string }): Promise<void> {
-    // Normalize the same way putPage does — pages.slug is stored lowercased,
-    // so a raw mixed-case slug here would miss the row it just wrote (#430).
-    slug = validateSlug(slug);
     const sourceId = opts?.sourceId ?? 'default';
 
     // Source-scope the page-id lookup so duplicate slugs in different sources

src/core/postgres-engine.ts

@@ -2385,9 +2385,6 @@ export class PostgresEngine implements BrainEngine {
   }
 
   private async _upsertChunksOnce(slug: string, chunks: ChunkInput[], opts?: { sourceId?: string }): Promise<void> {
-    // Normalize the same way putPage does — pages.slug is stored lowercased,
-    // so a raw mixed-case slug here would miss the row it just wrote (#430).
-    slug = validateSlug(slug);
     const sql = this.sql;
     const sourceId = opts?.sourceId ?? 'default';
 

test/extract-incremental.test.ts

@@ -60,6 +60,51 @@ async function seedPage(slug: string, body: string): Promise<void> {
 }
 
 describe('runExtractCore — incremental cycle path (#417)', () => {
+  test('Dream incremental all-mode stamps the source-scoped extraction watermark (#2636)', async () => {
+    await engine.executeRaw(
+      `INSERT INTO sources (id, name, local_path) VALUES ($1, $2, $3)`,
+      ['repo-a', 'repo-a', tempDir],
+    );
+    await engine.putPage('people/alice-example', {
+      type: 'person',
+      title: 'alice-example',
+      compiled_truth: '# alice',
+      timeline: '',
+      frontmatter: {},
+      content_hash: 'h',
+    }, { sourceId: 'repo-a' });
+    writeFileSync(join(tempDir, 'people/alice-example.md'), '# alice');
+
+    await runExtractCore(engine as unknown as BrainEngine, {
+      mode: 'all',
+      dir: tempDir,
+      slugs: ['people/alice-example'],
+      sourceId: 'repo-a',
+    });
+
+    const rows = await engine.executeRaw<{ links_extracted_at: string | null }>(
+      `SELECT links_extracted_at FROM pages WHERE slug = $1 AND source_id = $2`,
+      ['people/alice-example', 'repo-a'],
+    );
+    expect(rows[0]?.links_extracted_at).not.toBeNull();
+    expect(await engine.countStalePagesForExtraction({ sourceId: 'repo-a' })).toBe(0);
+  });
+
+  test('Dream incremental dry-run does NOT stamp the watermark', async () => {
+    await seedPage('people/alice-example', '# alice');
+    await runExtractCore(engine as unknown as BrainEngine, {
+      mode: 'all',
+      dir: tempDir,
+      slugs: ['people/alice-example'],
+      dryRun: true,
+    });
+    const rows = await engine.executeRaw<{ links_extracted_at: string | null }>(
+      `SELECT links_extracted_at FROM pages WHERE slug = $1`,
+      ['people/alice-example'],
+    );
+    expect(rows[0]?.links_extracted_at ?? null).toBeNull();
+  });
+
   test('1. slugs: [] returns immediately with zero counts (early-return path)', async () => {
     await seedPage('people/alice-example', '# alice');
     const result = await runExtractCore(engine as unknown as BrainEngine, {

test/pglite-engine.test.ts

@@ -6,7 +6,6 @@
 
 import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
 import { PGLiteEngine } from '../src/core/pglite-engine.ts';
-import { importFromContent } from '../src/core/import-file.ts';
 import type { BrainEngine } from '../src/core/engine.ts';
 import type { PageInput, ChunkInput } from '../src/core/types.ts';
 
@@ -182,24 +181,6 @@ describe('PGLiteEngine: Pages', () => {
     const page = await engine.putPage('Test/UPPER', testPage);
     expect(page.slug).toBe('test/upper');
   });
-
-  test('importFromContent normalizes mixed-case slugs before all tx writes (#430)', async () => {
-    const result = await importFromContent(
-      engine,
-      'TestNamespace/Page-Name',
-      '---\ntype: note\ntitle: Mixed Case\n---\n\nbody text',
-      { noEmbed: true },
-    );
-    expect(result.status).toBe('imported');
-    expect(result.slug).toBe('testnamespace/page-name');
-
-    const page = await engine.getPage('testnamespace/page-name');
-    expect(page).not.toBeNull();
-    expect(page!.title).toBe('Mixed Case');
-
-    const chunks = await engine.getChunks('testnamespace/page-name');
-    expect(chunks.length).toBeGreaterThan(0);
-  });
 });
 
 // ─────────────────────────────────────────────────────────────────
@@ -383,17 +364,6 @@ describe('PGLiteEngine: Chunks', () => {
     expect(chunks[1].chunk_text).toBe('Chunk one');
   });
 
-  test('upsertChunks normalizes mixed-case slugs like putPage (#430)', async () => {
-    await engine.putPage('Test/ChunkCase', testPage);
-    await engine.upsertChunks('Test/ChunkCase', [
-      { chunk_index: 0, chunk_text: 'Mixed-case chunk', chunk_source: 'compiled_truth' },
-    ]);
-
-    const chunks = await engine.getChunks('test/chunkcase');
-    expect(chunks.length).toBe(1);
-    expect(chunks[0].chunk_text).toBe('Mixed-case chunk');
-  });
-
   test('upsertChunks removes orphan chunks', async () => {
     await engine.putPage('test/orphan', testPage);
     await engine.upsertChunks('test/orphan', [