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>
