feat: restructure feature management and update project files

- Introduced a new `package-lock.json` to manage dependencies.
- Removed obsolete `.automaker/feature_list.json` and replaced it with a new structure under `.automaker/features/{id}/feature.json` for better organization.
- Updated various components to utilize the new features API for managing features, including creation, updates, and deletions.
- Enhanced the UI to reflect changes in feature management, including updates to the sidebar and board view.
- Improved documentation and comments throughout the codebase to clarify the new feature management process.

app/electron/services/mcp-server-stdio.js

@@ -144,7 +144,7 @@ async function handleToolsList(params, id) {
     tools: [
       {
         name: 'UpdateFeatureStatus',
-        description: 'Update the status of a feature in the feature list. Use this tool instead of directly modifying feature_list.json to safely update feature status. IMPORTANT: If the feature has skipTests=true, you should NOT mark it as verified - instead it will automatically go to waiting_approval status for manual review. Always include a summary of what was done.',
+        description: 'Update the status of a feature. Use this tool instead of directly modifying feature files to safely update feature status. IMPORTANT: If the feature has skipTests=true, you should NOT mark it as verified - instead it will automatically go to waiting_approval status for manual review. Always include a summary of what was done.',
         inputSchema: {
           type: 'object',
           properties: {