fix(resolution): stop "Resolving refs" wedge on theme-vendoring repos; add exclude config + index watchdogs (#999) (#1009)

Three fixes for a repo that commits a large JS/TS theme/SDK (Metronic under
static/, ~1,600 tracked files):

1. A SECOND "Resolving refs" quadratic that #915 didn't cover. #915 capped
   import-name collisions; this caps method-name collisions (init/update/render
   re-declared on every widget), which flow through matchMethodCall Strategy 3
   and findBestMatch instead. New AMBIGUOUS_NAME_CEILING (default 500, env
   CODEGRAPH_AMBIGUOUS_NAME_CEILING): above it the fuzzy strategies decline
   rather than score K candidates — no proximity score can pick the one true
   target among thousands anyway. Resolving drops from O(K^2) to linear in refs
   (e.g. 900-file synthetic: 28.7s -> 3.4s), edge counts unchanged, and the cap
   never fires on normal repos (max real method-collision ~40).

2. A new `exclude` array in codegraph.json keeps git-TRACKED paths out of the
   index, which .gitignore can't do (enumeration is `git ls-files`). Mirrors the
   existing includeIgnored plumbing across the git, sync, and non-git-walk
   paths.

3. `index`/`init` now install the #850 liveness + #277 ppid watchdogs (which
   were serve-only), so a wedged or orphaned indexer self-terminates instead of
   pinning a core. The --liftoff-only relaunch's spawnSync can't forward
   signals, so killing the parent shim used to orphan the worker.

Tests: ubiquitous-name ceiling, exclude (incl. tracked-file exclusion on git +
non-git), orphan self-termination (POSIX), and ppid-parser units. Shared the
ppid parsers out of mcp/index.ts into mcp/ppid-watchdog.ts.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

src/mcp/index.ts

@@ -50,18 +50,11 @@ import {
 import { connectWithHello, runLocalHandshakeProxy } from './proxy';
 import { getDaemonSocketPath } from './daemon-paths';
 import { getTelemetry } from '../telemetry';
-import { supervisionLostReason } from './ppid-watchdog';
+import { supervisionLostReason, parsePpidPollMs, parseHostPpid } from './ppid-watchdog';
 import { installMainThreadWatchdog, WatchdogHandle } from './liveness-watchdog';
 import { treatStdinFailureAsShutdown } from './stdin-teardown';
 import { HOST_PPID_ENV } from '../extraction/wasm-runtime-flags';
 
-/**
- * How often to poll `process.ppid` to detect parent process death (see #277).
- * 5s is a deliberate trade-off: the failure mode being guarded against is rare
- * (parent SIGKILL'd), and longer poll = less wakeup overhead while idle.
- */
-const DEFAULT_PPID_POLL_MS = 5000;
-
 /**
  * Env var that marks a process as the *detached daemon* itself (set by
  * {@link spawnDetachedDaemon} when it re-invokes the CLI). Without it a
@@ -94,34 +87,6 @@ const TAKEOVER_RETRY_DELAY_MS = 100;
 const DAEMON_CONNECT_MAX_RETRIES = 240;
 const DAEMON_CONNECT_RETRY_DELAY_MS = 25;
 
-/**
- * Resolve the PPID watchdog poll interval from an env override. A value of
- * `0` disables the watchdog entirely (escape hatch for embedded scenarios
- * where the parent legitimately re-parents the server on purpose). Anything
- * non-numeric or negative falls back to the default.
- */
-function parsePpidPollMs(raw: string | undefined): number {
-  if (raw === undefined || raw === '') return DEFAULT_PPID_POLL_MS;
-  const parsed = Number(raw);
-  if (!Number.isFinite(parsed)) return DEFAULT_PPID_POLL_MS;
-  if (parsed < 0) return DEFAULT_PPID_POLL_MS;
-  return Math.floor(parsed);
-}
-
-/**
- * Parse the host PID propagated across the `--liftoff-only` re-exec
- * ({@link HOST_PPID_ENV}). Returns a positive integer PID, or null when
- * unset/invalid — the direct-launch path, where the watchdog falls back to
- * `process.ppid` divergence. PIDs of 0/1 are rejected (0 = unknown, 1 = init,
- * i.e. already orphaned), so the watchdog doesn't latch onto init.
- */
-function parseHostPpid(raw: string | undefined): number | null {
-  if (raw === undefined || raw === '') return null;
-  const parsed = Number(raw);
-  if (!Number.isInteger(parsed) || parsed <= 1) return null;
-  return parsed;
-}
-
 /** Whether `CODEGRAPH_NO_DAEMON` was set to a truthy value. */
 function daemonOptOutSet(): boolean {
   const raw = process.env.CODEGRAPH_NO_DAEMON;

src/mcp/ppid-watchdog.ts

@@ -61,3 +61,35 @@ export function supervisionLostReason(state: SupervisionState): string | null {
   }
   return null;
 }
+
+/** Default PPID poll cadence (ms). Shared by the MCP server and CLI commands. */
+export const DEFAULT_PPID_POLL_MS = 5000;
+
+/**
+ * Resolve the PPID watchdog poll interval from an env override
+ * (`CODEGRAPH_PPID_POLL_MS`). A value of `0` disables the watchdog entirely
+ * (escape hatch for embedded scenarios where the parent legitimately re-parents
+ * the process on purpose). Anything non-numeric or negative falls back to the
+ * default.
+ */
+export function parsePpidPollMs(raw: string | undefined): number {
+  if (raw === undefined || raw === '') return DEFAULT_PPID_POLL_MS;
+  const parsed = Number(raw);
+  if (!Number.isFinite(parsed)) return DEFAULT_PPID_POLL_MS;
+  if (parsed < 0) return DEFAULT_PPID_POLL_MS;
+  return Math.floor(parsed);
+}
+
+/**
+ * Parse the host PID propagated across the `--liftoff-only` re-exec
+ * (`CODEGRAPH_HOST_PPID`). Returns a positive integer PID, or null when
+ * unset/invalid — the direct-launch path, where the watchdog falls back to
+ * `process.ppid` divergence. PIDs of 0/1 are rejected (0 = unknown, 1 = init,
+ * i.e. already orphaned), so the watchdog doesn't latch onto init.
+ */
+export function parseHostPpid(raw: string | undefined): number | null {
+  if (raw === undefined || raw === '') return null;
+  const parsed = Number(raw);
+  if (!Number.isInteger(parsed) || parsed <= 1) return null;
+  return parsed;
+}