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/@commander-js/extra-typings/index.js

@@ -0,0 +1,28 @@
+const commander = require('commander');
+
+exports = module.exports = {};
+
+// Return a different global program than commander,
+// and don't also return it as default export.
+exports.program = new commander.Command();
+
+/**
+ * Expose classes. The FooT versions are just types, so return Commander original implementations!
+ */
+
+exports.Argument = commander.Argument;
+exports.Command = commander.Command;
+exports.CommanderError = commander.CommanderError;
+exports.Help = commander.Help;
+exports.InvalidArgumentError = commander.InvalidArgumentError;
+exports.InvalidOptionArgumentError = commander.InvalidArgumentError; // Deprecated
+exports.Option = commander.Option;
+
+// In Commander, the create routines end up being aliases for the matching
+// methods on the global program due to the (deprecated) legacy default export.
+// Here we roll our own, the way Commander might in future.
+exports.createCommand = (name) => new commander.Command(name);
+exports.createOption = (flags, description) =>
+  new commander.Option(flags, description);
+exports.createArgument = (name, description) =>
+  new commander.Argument(name, description);