fix(indexing): HDD-class storage — false parse timeouts, dropped files, and WAL checkpoint write-back (#1231) (#1242)

Parse timeouts are now judged by the worker's own clock: the base timer
only marks a job late (after a long synchronous store stall, Node runs the
timers phase before the poll phase, so the timer fired before an
already-delivered result was processed — killing workers over parses that
took milliseconds, even on 0-byte files); a result arriving before a 3×
hard-kill backstop is accepted, timed-out files are retried, and
CODEGRAPH_PARSE_TIMEOUT_MS overrides the budget. Grammar WASM bytes are
pre-read once on the main thread and handed to every worker, so
spawns/respawns load grammars from memory instead of re-reading a
saturated disk.

Bulk indexing defers WAL auto-checkpointing for the whole run: the default
1000-page interval re-writes hot B-tree/FTS pages into the main DB file
over and over — ~95% of all disk I/O under throttled measurement. A
WalCheckpointValve bounds WAL growth with off-thread PASSIVE backfill
passes (never blocking the writer or the #850 watchdog heartbeat), pauses
the writer for a full backfill if the disk truly can't keep up, and folds
the WAL at the parse→resolution boundary so post-parse reads never page a
bulk-write-sized WAL. Opt out with CODEGRAPH_NO_WAL_DEFER=1; tune with
CODEGRAPH_WAL_VALVE_MB.

Measured at 150 IOPS (HDD class): commons-lang 1526s → 59s with 0 dropped
files (was 8); guava-scale completes in 7.6 min with a full graph where
v1.3.1 needed 25 min for a repo 5× smaller. Unthrottled: no change.

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

.dockerignore

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+node_modules
+dist
+.git
+.codegraph
+.kommandr
+docs
+assets