fix: harden daemon and large-index recovery paths (#1562)

* fix: harden indexing recovery and daemon liveness

* test: cover daemon and recovery review gaps

* test: pin that a failure marker never blocks a later successful parse (#1557 retry-discard guard)

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

---------

Co-authored-by: danusha2345 <ewidusoc498@gmail.com>
Co-authored-by: Colby McHenry <me@colbymchenry.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

__tests__/foundation.test.ts

@@ -120,6 +120,41 @@ describe('CodeGraph Foundation', () => {
       cg.close();
     });
 
+    it('restores every secondary index after a crash inside bulk parse load (#1556)', () => {
+      const dbPath = getDatabasePath(tempDir);
+      const first = DatabaseConnection.initialize(dbPath);
+      const before = (first.getDb()
+        .prepare("SELECT name FROM sqlite_master WHERE type = 'index' ORDER BY name")
+        .all() as Array<{ name: string }>).map((r) => r.name);
+      first.beginBulkParseLoad();
+      first.close();
+
+      const reopened = DatabaseConnection.open(dbPath);
+      const after = (reopened.getDb()
+        .prepare("SELECT name FROM sqlite_master WHERE type = 'index' ORDER BY name")
+        .all() as Array<{ name: string }>).map((r) => r.name);
+      reopened.close();
+
+      expect(after).toEqual(before);
+    });
+
+    it('skips secondary-index DDL when the schema is already healthy', () => {
+      const dbPath = getDatabasePath(tempDir);
+      const connection = DatabaseConnection.initialize(dbPath);
+      const db = connection.getDb();
+      const originalExec = db.exec.bind(db);
+      let execCalls = 0;
+      db.exec = (sql: string) => {
+        execCalls++;
+        originalExec(sql);
+      };
+
+      (connection as any).healBulkSecondaryIndexes();
+      connection.close();
+
+      expect(execCalls).toBe(0);
+    });
+
     it('should return correct database size', () => {
       const cg = CodeGraph.initSync(tempDir);
       const stats = cg.getStats();