fix(watcher): exclude ignored dirs before watching to prevent inotify exhaustion (#276)

The file watcher registered a recursive watch over the entire project (node_modules, build output, caches included) and filtered only in the callback — exhausting the Linux inotify budget on large repos (#276). It now uses chokidar and excludes the same directories the indexer ignores (built-in default-ignore set + the project .gitignore) BEFORE registering a watch, so the watch count on a 900-dir node_modules drops from ~1200 to ~14 even with no .gitignore. Stacks with the shared daemon (#411): one watcher across agents, now small.

Also hardens the #411 daemon lockfile against a concurrent-startup race the new watcher timing made reproducible — the lock is now created atomically with its content (temp-write + hard-link), so racing daemons can never both win. Validated on macOS, Linux (Docker), and Windows (chokidar + fs.linkSync on NTFS).

Co-Authored-By: Colby McHenry <me@colbymchenry.com>
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

package-lock.json

@@ -1,15 +1,16 @@
 {
   "name": "@colbymchenry/codegraph",
-  "version": "0.9.3",
+  "version": "0.9.4",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "@colbymchenry/codegraph",
-      "version": "0.9.3",
+      "version": "0.9.4",
       "license": "MIT",
       "dependencies": {
         "@clack/prompts": "^1.3.0",
+        "chokidar": "^4.0.3",
         "commander": "^14.0.2",
         "fast-string-width": "^3.0.2",
         "fast-wrap-ansi": "^0.2.0",
@@ -1004,6 +1005,21 @@
         "node": ">= 16"
       }
     },
+    "node_modules/chokidar": {
+      "version": "4.0.3",
+      "resolved": "https://registry.npmjs.org/chokidar/-/chokidar-4.0.3.tgz",
+      "integrity": "sha512-Qgzu8kfBvo+cA4962jnP1KkS6Dop5NS6g7R5LFYJr4b8Ub94PPQXUksCw9PvXoeXPRRddRNC5C1JQUR2SMGtnA==",
+      "license": "MIT",
+      "dependencies": {
+        "readdirp": "^4.0.1"
+      },
+      "engines": {
+        "node": ">= 14.16.0"
+      },
+      "funding": {
+        "url": "https://paulmillr.com/funding/"
+      }
+    },
     "node_modules/commander": {
       "version": "14.0.3",
       "resolved": "https://registry.npmjs.org/commander/-/commander-14.0.3.tgz",
@@ -1269,6 +1285,19 @@
         "node": "^10 || ^12 || >=14"
       }
     },
+    "node_modules/readdirp": {
+      "version": "4.1.2",
+      "resolved": "https://registry.npmjs.org/readdirp/-/readdirp-4.1.2.tgz",
+      "integrity": "sha512-GDhwkLfywWL2s6vEjyhri+eXmfH6j1L7JE27WhqLeYzoh/A3DBaYGEj2H/HFZCn/kMfim73FXxEJTw06WtxQwg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 14.18.0"
+      },
+      "funding": {
+        "type": "individual",
+        "url": "https://paulmillr.com/funding/"
+      }
+    },
     "node_modules/rollup": {
       "version": "4.57.1",
       "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.57.1.tgz",