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/yaml/dist/log.js

@@ -0,0 +1,19 @@
+'use strict';
+
+var node_process = require('process');
+
+function debug(logLevel, ...messages) {
+    if (logLevel === 'debug')
+        console.log(...messages);
+}
+function warn(logLevel, warning) {
+    if (logLevel === 'debug' || logLevel === 'warn') {
+        if (typeof node_process.emitWarning === 'function')
+            node_process.emitWarning(warning);
+        else
+            console.warn(warning);
+    }
+}
+
+exports.debug = debug;
+exports.warn = warn;