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/_customOmitClone.js

@@ -0,0 +1,16 @@
+import isPlainObject from './isPlainObject.js';
+
+/**
+ * Used by `_.omit` to customize its `_.cloneDeep` use to only clone plain
+ * objects.
+ *
+ * @private
+ * @param {*} value The value to inspect.
+ * @param {string} key The key of the property to inspect.
+ * @returns {*} Returns the uncloned value or `undefined` to defer cloning to `_.cloneDeep`.
+ */
+function customOmitClone(value) {
+  return isPlainObject(value) ? undefined : value;
+}
+
+export default customOmitClone;