fix(watcher): bound fd/watch cost with a native fs.watch hybrid (#644, #496, #555, #628, #579) (#650)

chokidar v4 holds one OS file descriptor per watched file on macOS (libuv's
kqueue backend registers an fd per vnode; fsevents is installed but v4 no
longer uses it). On a large project the `serve --mcp` daemon accumulated tens
of thousands of open REG descriptors and exhausted kern.maxfiles — crashing
unrelated processes system-wide with ENFILE. #276 only trimmed the count by
ignoring directories; the source tree still cost one fd per file.

Replace chokidar with a pure-JS native fs.watch hybrid, keeping codegraph's
zero-native-addon "any OS builds any bundle" invariant:

  - macOS / Windows: a single recursive fs.watch (one FSEvents stream /
    ReadDirectoryChangesW handle) -> O(1) descriptors regardless of repo size.
  - Linux: one inotify watch per directory (O(dirs), dynamic add for new
    dirs, capped via CODEGRAPH_MAX_DIR_WATCHES) instead of per-file watches.

Validated empirically: macOS 0 extra fds at 6k and 12k files; Linux 31 inotify
watches at 6k files (per-file would be 6k); Windows recursive catches nested
and new-directory edits. Full test suite green.

Tests drive the watcher through an inertForTests seam (no OS watcher) for
determinism under parallel vitest, with one real-fs end-to-end test exercising
the genuine native path.

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

CHANGELOG.md

@@ -9,6 +9,9 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+### Fixes
+
+- The background file watcher no longer exhausts your machine's file-descriptor budget. On macOS it previously kept **one open file handle per watched file**, so on a large project the running MCP server could pile up tens of thousands of handles and blow past the system-wide limit — at which point *unrelated* apps (your shell, editor, Docker, browser) started failing with "too many open files" until the codegraph process was killed. The watcher now uses a single recursive watch on macOS and Windows, and bounded per-directory watches on Linux, so its cost stays flat no matter how large the project is. (#644, #496, #555, #628, #579)
 
 ## [0.9.9] - 2026-06-02