fix: keep only source-map extracted node_modules, exclude pnpm artifacts

Restore node_modules to exact state from cli.js.map extraction:
- Move .ignored/ and .ignored_* files back to original package paths
- Remove pnpm symlinks (replaced by real source-map directories)
- Update .gitignore: only exclude /dist/, .pnpm/, .bin/, .ignored* dirs
- All package dist/ folders are now preserved as part of source-map files

After clone, run `pnpm install` to get pnpm-managed symlinks for building.
The committed node_modules contains the original TypeScript/JS source files
as bundled in cli.js.

claude-code-source/node_modules/lodash-es/_nativeKeysIn.js

@@ -0,0 +1,20 @@
+/**
+ * This function is like
+ * [`Object.keys`](http://ecma-international.org/ecma-262/7.0/#sec-object.keys)
+ * except that it includes inherited enumerable properties.
+ *
+ * @private
+ * @param {Object} object The object to query.
+ * @returns {Array} Returns the array of property names.
+ */
+function nativeKeysIn(object) {
+  var result = [];
+  if (object != null) {
+    for (var key in Object(object)) {
+      result.push(key);
+    }
+  }
+  return result;
+}
+
+export default nativeKeysIn;