fix: Add cleanup of obsolete files during ccw install reinstallation

- Add getFileReferenceCounts() to track file references across manifests
- Add cleanupOldFiles() to remove files not in new installation
- Protect shared files referenced by other installations (Global/Path)
- Display cleanup statistics in installation summary

Previously, reinstalling would only overwrite existing files but leave
obsolete files that were removed from source. Now properly cleans up
while protecting files shared between Global and Path installations.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

ccw/src/core/manifest.ts

@@ -229,3 +229,43 @@ export function deleteManifest(manifestFile: string): void {
 export function getManifestDir(): string {
   return MANIFEST_DIR;
 }
+
+/**
+ * Get file reference counts across all manifests
+ * Returns a map of file path -> array of manifest IDs that reference it
+ * @param excludeManifestId - Optional manifest ID to exclude from counting
+ * @returns Map of file paths to referencing manifest IDs
+ */
+export function getFileReferenceCounts(excludeManifestId?: string): Map<string, string[]> {
+  const fileRefs = new Map<string, string[]>();
+  const manifests = getAllManifests();
+
+  for (const manifest of manifests) {
+    // Skip the excluded manifest (usually the one being replaced)
+    if (excludeManifestId && manifest.manifest_id === excludeManifestId) {
+      continue;
+    }
+
+    for (const fileEntry of manifest.files || []) {
+      const normalizedPath = fileEntry.path.toLowerCase().replace(/\\/g, '/');
+      const refs = fileRefs.get(normalizedPath) || [];
+      refs.push(manifest.manifest_id);
+      fileRefs.set(normalizedPath, refs);
+    }
+  }
+
+  return fileRefs;
+}
+
+/**
+ * Check if a file is referenced by other installations
+ * @param filePath - File path to check
+ * @param excludeManifestId - Manifest ID to exclude from checking
+ * @returns True if file is referenced by other installations
+ */
+export function isFileReferencedByOthers(filePath: string, excludeManifestId: string): boolean {
+  const fileRefs = getFileReferenceCounts(excludeManifestId);
+  const normalizedPath = filePath.toLowerCase().replace(/\\/g, '/');
+  const refs = fileRefs.get(normalizedPath) || [];
+  return refs.length > 0;
+}