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/queries.ts

@@ -880,6 +880,37 @@ export class QueryBuilder {
     return rows.map(rowToNode);
   }
 
+  /**
+   * Stream nodes of one language whose `decorators` JSON array contains
+   * `decorator`. The LIKE on the JSON text is a cheap index-free pre-filter
+   * (a decorator name can appear as a substring of another), so callers must
+   * still exact-check `node.decorators.includes(decorator)`. Exists so the
+   * kotlin expect/actual synthesizer never materializes the whole node table
+   * the way `getAllNodes().filter(...)` did — that array alone OOM'd Node's
+   * default heap on a 2M-node graph (#1212).
+   */
+  *iterateNodesByLanguageWithDecorator(language: Language, decorator: string): IterableIterator<Node> {
+    // Fresh statement per call — an iterator holds an open cursor (see
+    // iterateNodesByKind).
+    const stmt = this.db.prepare(
+      "SELECT * FROM nodes WHERE language = ? AND decorators LIKE '%' || ? || '%'"
+    );
+    for (const row of stmt.iterate(language, `"${decorator}"`)) {
+      yield rowToNode(row as NodeRow);
+    }
+  }
+
+  /**
+   * Distinct languages present in the files table. One indexed aggregate —
+   * lets the dynamic-edge synthesizers skip passes for languages the project
+   * doesn't contain at all (a Kotlin pass has no work on a pure-C repo), so
+   * their cost is zero rather than a full-graph scan that finds nothing (#1212).
+   */
+  getDistinctFileLanguages(): Set<string> {
+    const rows = this.db.prepare('SELECT DISTINCT language FROM files').all() as Array<{ language: string }>;
+    return new Set(rows.map((r) => r.language));
+  }
+
   /**
    * Get nodes by exact name match (uses idx_nodes_name index)
    */
@@ -1853,6 +1884,19 @@ export class QueryBuilder {
     return rows.map((r) => r.name);
   }
 
+  /**
+   * Stream the distinct node names one row at a time — the incremental
+   * counterpart to {@link getAllNodeNames} for callers that need to yield
+   * to the event loop mid-scan (resolver cache warm-up on multi-million-node
+   * indexes). Fresh statement per call: the iterator holds an open cursor.
+   */
+  *iterateNodeNames(): IterableIterator<string> {
+    const stmt = this.db.prepare('SELECT DISTINCT name FROM nodes');
+    for (const row of stmt.iterate()) {
+      yield (row as { name: string }).name;
+    }
+  }
+
   /**
    * Get unresolved references scoped to specific file paths.
    * Uses the idx_unresolved_file_path index for efficient lookup.