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/xmlbuilder/lib/XMLDOMConfiguration.js

@@ -0,0 +1,80 @@
+// Generated by CoffeeScript 2.4.1
+(function() {
+  var XMLDOMConfiguration, XMLDOMErrorHandler, XMLDOMStringList;
+
+  XMLDOMErrorHandler = require('./XMLDOMErrorHandler');
+
+  XMLDOMStringList = require('./XMLDOMStringList');
+
+  // Implements the DOMConfiguration interface
+  module.exports = XMLDOMConfiguration = (function() {
+    class XMLDOMConfiguration {
+      constructor() {
+        var clonedSelf;
+        this.defaultParams = {
+          "canonical-form": false,
+          "cdata-sections": false,
+          "comments": false,
+          "datatype-normalization": false,
+          "element-content-whitespace": true,
+          "entities": true,
+          "error-handler": new XMLDOMErrorHandler(),
+          "infoset": true,
+          "validate-if-schema": false,
+          "namespaces": true,
+          "namespace-declarations": true,
+          "normalize-characters": false,
+          "schema-location": '',
+          "schema-type": '',
+          "split-cdata-sections": true,
+          "validate": false,
+          "well-formed": true
+        };
+        this.params = clonedSelf = Object.create(this.defaultParams);
+      }
+
+      // Gets the value of a parameter.
+
+      // `name` name of the parameter
+      getParameter(name) {
+        if (this.params.hasOwnProperty(name)) {
+          return this.params[name];
+        } else {
+          return null;
+        }
+      }
+
+      // Checks if setting a parameter to a specific value is supported.
+
+      // `name` name of the parameter
+      // `value` parameter value
+      canSetParameter(name, value) {
+        return true;
+      }
+
+      // Sets the value of a parameter.
+
+      // `name` name of the parameter
+      // `value` new value or null if the user wishes to unset the parameter
+      setParameter(name, value) {
+        if (value != null) {
+          return this.params[name] = value;
+        } else {
+          return delete this.params[name];
+        }
+      }
+
+    };
+
+    // Returns the list of parameter names
+    Object.defineProperty(XMLDOMConfiguration.prototype, 'parameterNames', {
+      get: function() {
+        return new XMLDOMStringList(Object.keys(this.defaultParams));
+      }
+    });
+
+    return XMLDOMConfiguration;
+
+  }).call(this);
+
+}).call(this);