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/cloneDeep.js

@@ -0,0 +1,29 @@
+import baseClone from './_baseClone.js';
+
+/** Used to compose bitmasks for cloning. */
+var CLONE_DEEP_FLAG = 1,
+    CLONE_SYMBOLS_FLAG = 4;
+
+/**
+ * This method is like `_.clone` except that it recursively clones `value`.
+ *
+ * @static
+ * @memberOf _
+ * @since 1.0.0
+ * @category Lang
+ * @param {*} value The value to recursively clone.
+ * @returns {*} Returns the deep cloned value.
+ * @see _.clone
+ * @example
+ *
+ * var objects = [{ 'a': 1 }, { 'b': 2 }];
+ *
+ * var deep = _.cloneDeep(objects);
+ * console.log(deep[0] === objects[0]);
+ * // => false
+ */
+function cloneDeep(value) {
+  return baseClone(value, CLONE_DEEP_FLAG | CLONE_SYMBOLS_FLAG);
+}
+
+export default cloneDeep;