fix(extract): preserve facts on parse warnings (#3494)

src/core/cycle/extract-facts.ts

@@ -17,11 +17,12 @@
  *      DB rows need cleanup (#1781 — the unconditional wipe-and-reinsert
  *      made every cycle non-idempotent, re-appending duplicate rows).
  *
- * After the phase, the DB index for every affected page matches the
- * fence's canonical (claim, source) row set (modulo embeddings +
- * runtime-derived fields). Pages with no fence wipe DB rows for that
- * page coordinate only; legacy NULL-source_markdown_slug rows survive
- * because deleteFactsForPage targets source_markdown_slug = slug only.
+ * After the phase, the DB index for every cleanly parsed affected page
+ * matches the fence's canonical (claim, source) row set (modulo embeddings
+ * + runtime-derived fields). Warning-bearing parses are non-authoritative
+ * and preserve that page's existing index. Pages with no fence wipe DB rows
+ * for that page coordinate only; legacy NULL-source_markdown_slug rows
+ * survive because deleteFactsForPage targets source_markdown_slug = slug only.
  *
  * Empty-fence guard (Codex R2-#7; #2484; #2646): the phase refuses to do
  * its destructive reconciliation pass when genuinely-backfillable legacy
@@ -333,6 +334,11 @@ export async function runExtractFacts(
       result.warnings.push(
         ...parsed.warnings.map(w => `${slug}: ${w}`),
       );
+      // The parser deliberately skips malformed rows and returns any rows it
+      // could still recover. That partial result is not authoritative: using
+      // it for reconciliation would interpret skipped rows as deletions.
+      // Preserve this page's existing index and continue with other pages.
+      continue;
     }
 
     if (parsed.facts.length > 0) result.pagesWithFacts += 1;

test/extract-facts-phase.test.ts

@@ -231,6 +231,44 @@ describe('runExtractFacts — happy path', () => {
     expect(rows.rows[0].fact).toBe('A');
   });
 
+  test('malformed fence rows make the page non-authoritative and preserve its indexed facts', async () => {
+    await putPage('people/alice', FACT_FENCE(
+      `| 1 | A | fact | 1.0 | world | medium | 2026-01-01 |  | s |  |
+| 2 | B | fact | 1.0 | world | medium | 2026-01-01 |  | s |  |`,
+    ));
+    await runExtractFacts(engine, { slugs: ['people/alice'] });
+
+    // A hand edit corrupts row 2. The parser can still recover row 1, but
+    // that partial result is not an authoritative replacement for the page.
+    await putPage('people/alice', FACT_FENCE(
+      `| 1 | A | fact | 1.0 | world | medium | 2026-01-01 |  | s |  |
+| 2 | B | bogus | 1.0 | world | medium | 2026-01-01 |  | s |  |`,
+    ));
+    await putPage('people/bob', FACT_FENCE(
+      `| 1 | Clean | fact | 1.0 | world | medium | 2026-01-01 |  | s |  |`,
+    ));
+
+    const r = await runExtractFacts(engine, { slugs: ['people/alice', 'people/bob'] });
+
+    expect(r.warnings.some(w => w.includes('FACTS_TABLE_MALFORMED'))).toBe(true);
+    expect(r.pagesScanned).toBe(2);
+    expect(r.factsInserted).toBe(1);
+    expect(r.factsDeleted).toBe(0);
+
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const rows = await (engine as any).db.query(
+      `SELECT fact FROM facts WHERE source_markdown_slug = 'people/alice' ORDER BY row_num`,
+    );
+    expect(rows.rows.map((row: { fact: string }) => row.fact)).toEqual(['A', 'B']);
+
+    // A warning is page-local: clean pages in the same cycle still reconcile.
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const cleanRows = await (engine as any).db.query(
+      `SELECT fact FROM facts WHERE source_markdown_slug = 'people/bob'`,
+    );
+    expect(cleanRows.rows.map((row: { fact: string }) => row.fact)).toEqual(['Clean']);
+  });
+
   test('page with no facts fence → DB facts for that page wiped (empty fence reconciles to empty index)', async () => {
     await putPage('people/alice', FACT_FENCE(
       `| 1 | seeded | fact | 1.0 | world | medium | 2026-01-01 |  | s |  |`,