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>

__tests__/db-perf.test.ts

@@ -233,21 +233,22 @@ describe('runMaintenance', () => {
     if (fs.existsSync(dir)) fs.rmSync(dir, { recursive: true, force: true });
   });
 
-  it('runs without throwing on a fresh database', () => {
-    expect(() => db.runMaintenance()).not.toThrow();
+  it('runs without throwing on a fresh database', async () => {
+    await expect(db.runMaintenance()).resolves.toBeUndefined();
   });
 
-  it('runs without throwing after writes', () => {
+  it('runs without throwing after writes', async () => {
     const q = new QueryBuilder(db.getDb());
     q.insertNodes([makeNode('n1'), makeNode('n2')]);
-    expect(() => db.runMaintenance()).not.toThrow();
+    await expect(db.runMaintenance()).resolves.toBeUndefined();
   });
 
-  it('swallows failures rather than propagating (best-effort)', () => {
+  it('swallows failures rather than propagating (best-effort)', async () => {
     // Close the DB so the underlying handle would normally throw on any
-    // exec(). runMaintenance must still not propagate.
+    // exec(). runMaintenance (worker on its own connection, or the in-line
+    // fallback) must still not propagate.
     db.close();
-    expect(() => db.runMaintenance()).not.toThrow();
+    await expect(db.runMaintenance()).resolves.toBeUndefined();
   });
 });