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/now.js

@@ -0,0 +1,23 @@
+import root from './_root.js';
+
+/**
+ * Gets the timestamp of the number of milliseconds that have elapsed since
+ * the Unix epoch (1 January 1970 00:00:00 UTC).
+ *
+ * @static
+ * @memberOf _
+ * @since 2.4.0
+ * @category Date
+ * @returns {number} Returns the timestamp.
+ * @example
+ *
+ * _.defer(function(stamp) {
+ *   console.log(_.now() - stamp);
+ * }, _.now());
+ * // => Logs the number of milliseconds it took for the deferred invocation.
+ */
+var now = function() {
+  return root.Date.now();
+};
+
+export default now;