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/compose/compose-doc.js

@@ -0,0 +1,45 @@
+'use strict';
+
+var Document = require('../doc/Document.js');
+var composeNode = require('./compose-node.js');
+var resolveEnd = require('./resolve-end.js');
+var resolveProps = require('./resolve-props.js');
+
+function composeDoc(options, directives, { offset, start, value, end }, onError) {
+    const opts = Object.assign({ _directives: directives }, options);
+    const doc = new Document.Document(undefined, opts);
+    const ctx = {
+        atKey: false,
+        atRoot: true,
+        directives: doc.directives,
+        options: doc.options,
+        schema: doc.schema
+    };
+    const props = resolveProps.resolveProps(start, {
+        indicator: 'doc-start',
+        next: value ?? end?.[0],
+        offset,
+        onError,
+        parentIndent: 0,
+        startOnNewline: true
+    });
+    if (props.found) {
+        doc.directives.docStart = true;
+        if (value &&
+            (value.type === 'block-map' || value.type === 'block-seq') &&
+            !props.hasNewline)
+            onError(props.end, 'MISSING_CHAR', 'Block collection cannot start on same line with directives-end marker');
+    }
+    // @ts-expect-error If Contents is set, let's trust the user
+    doc.contents = value
+        ? composeNode.composeNode(ctx, value, props, onError)
+        : composeNode.composeEmptyNode(ctx, props.end, start, null, props, onError);
+    const contentEnd = doc.contents.range[2];
+    const re = resolveEnd.resolveEnd(end, contentEnd, false, onError);
+    if (re.comment)
+        doc.comment = re.comment;
+    doc.range = [offset, contentEnd, re.offset];
+    return doc;
+}
+
+exports.composeDoc = composeDoc;