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__/query-pool.test.ts

@@ -171,4 +171,28 @@ describe('QueryPool', () => {
     expect(res.isError).toBe(true);
     expect(pool.healthy).toBe(false);
   });
+
+  it('is not `ready` until a worker completes its cold start (#662 first-call stall)', async () => {
+    // A worker cold start is seconds (tens under load); a call queued behind it
+    // waits for the 45s busy backstop with nothing served. The ToolHandler must
+    // be able to see "no warm worker yet" and dispatch in-process instead — so
+    // `ready` is false before the first 'ready' handshake and true after.
+    // (FakeWorker posts 'ready' on a macrotask — the synchronous check below
+    // observes the cold-start window.)
+    const pool = new QueryPool({ root: '/x', size: 1, createWorker: () => new FakeWorker((m) => ({ result: ok(`r:${m.toolName}`) })) });
+    expect(pool.ready).toBe(false); // eager worker spawned but not yet warm
+    await sleep(5);                 // let the ready handshake land
+    expect(pool.ready).toBe(true);
+    const res = await pool.run('codegraph_status', {});
+    expect(res.content[0].text).toBe('r:codegraph_status');
+    await pool.destroy();
+    expect(pool.ready).toBe(false); // destroyed pool must not be selected
+  });
+
+  it('a failed cold start (ready ok:false) does not mark the pool ready', async () => {
+    const pool = new QueryPool({ root: '/x', size: 1, createWorker: () => new FakeWorker(() => ({ hang: true }), /* readyOk */ false) });
+    await sleep(5);
+    expect(pool.ready).toBe(false); // hard open failure — keep serving in-process
+    await pool.destroy();
+  });
 });