fix(indexing): bounded-memory yielding pipeline tail + daemon session fixes (#1212) (#1226)

Large-codebase indexing died at the end of "Resolving refs" two ways:
watchdog kills of healthy work (24k-file Java on Windows, #1212 — third
iteration of the #1091/#1122 class) and hard OOMs (Linux kernel scale,
where v1.3.0 could not complete at any watchdog setting). Root causes:
~31 of 37 dynamic-edge synthesis passes ran start-to-finish with no
yield points, several materialized whole-graph snapshots (kotlin
expect/actual opened with getAllNodes() — 2M nodes in one array; the
C fn-pointer pass retained every C file's contents twice plus every
function node), and the post-index WAL checkpoint ran minutes of
synchronous IO on the main thread, killing even a successful index at
the finish line.

The pipeline tail now follows the same discipline as the rest: never
hold O(graph) in the heap, yield everywhere.

- All synthesis passes stream node-kind scans (cursors, not arrays) and
  yield on time-budgeted checkpoints; language gates skip passes whose
  filters a project's file languages provably can't satisfy.
- kotlin expect/actual filters SQL-side; c-fnptr caches are LRU-bounded,
  units stream one file at a time, and the all-functions array +
  write-only id map are gone; spring reads each .java once, not twice.
- runMaintenance moved to a worker thread (own SQLite connection);
  per-file store commits chunk with yields behind a serialized flush
  chain (preserving #1015 file-order determinism); resolver warm-up
  streams the DISTINCT name set; resolution batch-tail and merged-edge
  inserts run in bounded sub-transactions.
- Daemon: fixed a socket-handoff race that could leave a fresh MCP
  session permanently silent (client-hello tail unshifted into a
  flowing stream with zero listeners — the long-standing #662 test
  flake was this real bug); first tool call no longer queues behind
  the query pool's cold start (pool.ready gate).

Validation: Linux kernel (70,129 files, 2.05M nodes, 6.4M edges) fully
indexes in 27m8s on a 2-core/6GB container at default heap + default
watchdog; llvm-project (180k files) completes under 1GB RSS including
kill-and-sync recovery; synthesized-edge and full-graph parity are
byte-identical vs baseline on elasticsearch/redis/vim; the ex-flaky
daemon test passed 25/25 under load. Env-gated diagnostics kept:
CODEGRAPH_SYNTH_TIMINGS pass/phase timings, CODEGRAPH_MCP_DEBUG hop
tracing. Design record: docs/design/main-thread-stall-followup.md.

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

src/db/index.ts

@@ -198,8 +198,8 @@ export class DatabaseConnection {
   }
 
   /**
-   * Lightweight, non-blocking maintenance to run after bulk writes
-   * (indexAll, sync). Two operations:
+   * Lightweight maintenance to run after bulk writes (indexAll, sync).
+   * Two operations:
    *
    *   - `PRAGMA optimize` — incremental ANALYZE; SQLite only re-analyzes
    *     tables whose row counts changed materially since the last
@@ -211,19 +211,60 @@ export class DatabaseConnection {
    *     unboundedly between automatic checkpoints (auto-fires at 1000
    *     pages by default; large indexAll runs blow past that).
    *
-   * Both operations are silently swallowed on failure — they're a
-   * best-effort optimization, never load-bearing for correctness.
+   * Runs on a WORKER THREAD with its own connection: on a multi-GB index
+   * these pragmas are minutes of synchronous IO (a 95k-file kernel index
+   * left a 593MB WAL whose checkpoint alone blew the #850 watchdog's 60s
+   * window and got a COMPLETED index SIGKILLed at the finish line). WAL
+   * checkpointing from a second connection is standard SQLite; `PRAGMA
+   * optimize` persists its statistics in sqlite_stat tables, so the main
+   * connection benefits the same. The main thread just awaits a message,
+   * so the event loop — and the watchdog heartbeat — keep turning.
+   *
+   * Everything is silently swallowed on failure — best-effort
+   * optimization, never load-bearing for correctness. If worker threads
+   * are unavailable, falls back to a bounded in-line `PRAGMA optimize`
+   * and SKIPS the checkpoint (the final close() checkpoints after the
+   * CLI has already disarmed its watchdog).
    */
-  runMaintenance(): void {
-    try {
-      this.db.exec('PRAGMA optimize');
-    } catch {
-      // ignore
+  async runMaintenance(): Promise<void> {
+    // In-memory / test databases: nothing worth a worker round-trip.
+    if (!this.dbPath || this.dbPath === ':memory:') {
+      try { this.db.exec('PRAGMA optimize'); } catch { /* ignore */ }
+      try { this.db.exec('PRAGMA wal_checkpoint(PASSIVE)'); } catch { /* ignore */ }
+      return;
     }
     try {
-      this.db.exec('PRAGMA wal_checkpoint(PASSIVE)');
+      const { Worker } = await import('node:worker_threads');
+      const workerSource = `
+        const { workerData, parentPort } = require('node:worker_threads');
+        try {
+          const { DatabaseSync } = require('node:sqlite');
+          const db = new DatabaseSync(workerData.dbPath);
+          try { db.exec('PRAGMA analysis_limit=1000'); } catch {}
+          try { db.exec('PRAGMA optimize'); } catch {}
+          try { db.exec('PRAGMA wal_checkpoint(PASSIVE)'); } catch {}
+          try { db.close(); } catch {}
+        } catch {}
+        parentPort.postMessage('done');
+      `;
+      await new Promise<void>((resolve) => {
+        let settled = false;
+        const finish = (): void => {
+          if (!settled) { settled = true; resolve(); }
+        };
+        try {
+          const worker = new Worker(workerSource, { eval: true, workerData: { dbPath: this.dbPath } });
+          worker.once('message', () => { void worker.terminate(); finish(); });
+          worker.once('error', () => { void worker.terminate(); finish(); });
+          worker.once('exit', finish);
+        } catch {
+          finish();
+        }
+      });
     } catch {
-      // ignore (e.g., not in WAL mode)
+      // Worker threads unavailable — bounded in-line fallback, no checkpoint.
+      try { this.db.exec('PRAGMA analysis_limit=1000'); } catch { /* ignore */ }
+      try { this.db.exec('PRAGMA optimize'); } catch { /* ignore */ }
     }
   }