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>

src/db/index.ts

@@ -145,6 +145,7 @@ export class DatabaseConnection {
     // beginBulkNodeLoad and endBulkNodeLoad): the FTS triggers are missing and
     // nodes_fts is stale. Rebuild + recreate so search stays in sync.
     conn.healBulkNodeLoad();
+    conn.healBulkSecondaryIndexes();
 
     // Self-heal a killed session's leftover oversized WAL (#1431) — one
     // statSync when healthy, off-thread checkpoint+truncate when not.
@@ -363,6 +364,28 @@ export class DatabaseConnection {
     this.endBulkNodeLoad();
   }
 
+  /** Recreate every secondary index a killed bulk parse/ref/edge window may leave dropped. */
+  private healBulkSecondaryIndexes(): void {
+    const names = [...new Set<string>([
+      ...DatabaseConnection.BULK_PARSE_INDEX_NAMES,
+      ...DatabaseConnection.BULK_REF_INDEX_NAMES,
+      ...DatabaseConnection.BULK_EDGE_INDEX_NAMES,
+    ])];
+    const placeholders = names.map(() => '?').join(',');
+    const row = this.db
+      .prepare(`SELECT count(*) AS c FROM sqlite_master WHERE type = 'index' AND name IN (${placeholders})`)
+      .get(...names) as { c: number } | undefined;
+    if ((row?.c ?? 0) >= names.length) return;
+
+    const schemaPath = path.join(__dirname, 'schema.sql');
+    const schema = fs.readFileSync(schemaPath, 'utf-8');
+    for (const idx of names) {
+      const m = schema.match(new RegExp(`CREATE INDEX IF NOT EXISTS ${idx}\\b[^;]*;`));
+      if (!m) throw new Error(`schema.sql: index ${idx} not found for crash recovery`);
+      this.db.exec(m[0]);
+    }
+  }
+
   /**
    * Recreate the FTS sync triggers from schema.sql — extracted from the file
    * rather than duplicated here so the DDL cannot drift from the schema.