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>

__tests__/ppid-watchdog.test.ts

@@ -10,7 +10,7 @@
  * stubbing `isAlive` and `platform`.
  */
 import { describe, it, expect } from 'vitest';
-import { supervisionLostReason } from '../src/mcp/ppid-watchdog';
+import { supervisionLostReason, parsePpidPollMs, parseHostPpid, DEFAULT_PPID_POLL_MS } from '../src/mcp/ppid-watchdog';
 
 const alive = () => true;
 const dead = () => false;
@@ -136,3 +136,32 @@ describe('supervisionLostReason', () => {
     });
   });
 });
+
+describe('parsePpidPollMs', () => {
+  it('defaults when unset / empty / non-numeric / negative', () => {
+    expect(parsePpidPollMs(undefined)).toBe(DEFAULT_PPID_POLL_MS);
+    expect(parsePpidPollMs('')).toBe(DEFAULT_PPID_POLL_MS);
+    expect(parsePpidPollMs('abc')).toBe(DEFAULT_PPID_POLL_MS);
+    expect(parsePpidPollMs('-5')).toBe(DEFAULT_PPID_POLL_MS);
+  });
+  it('honours a positive override and floors it', () => {
+    expect(parsePpidPollMs('200')).toBe(200);
+    expect(parsePpidPollMs('150.9')).toBe(150);
+  });
+  it('treats 0 as the explicit "disable" sentinel (caller skips the timer)', () => {
+    expect(parsePpidPollMs('0')).toBe(0);
+  });
+});
+
+describe('parseHostPpid', () => {
+  it('returns null for unset / empty / non-integer / orphan-sentinel pids', () => {
+    expect(parseHostPpid(undefined)).toBeNull();
+    expect(parseHostPpid('')).toBeNull();
+    expect(parseHostPpid('x')).toBeNull();
+    expect(parseHostPpid('0')).toBeNull();  // unknown
+    expect(parseHostPpid('1')).toBeNull();  // init = already orphaned
+  });
+  it('returns a real positive pid', () => {
+    expect(parseHostPpid('4242')).toBe(4242);
+  });
+});