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/src/components/views/agent-tools-view.tsx

@@ -155,7 +155,7 @@ export function AgentToolsView() {
       // In mock mode, simulate terminal output
       // In real Electron mode, this would use child_process
       const mockOutputs: Record<string, string> = {
-        ls: "app_spec.txt\nfeature_list.json\nnode_modules\npackage.json\nsrc\ntests\ntsconfig.json",
+        ls: "app_spec.txt\nfeatures\nnode_modules\npackage.json\nsrc\ntests\ntsconfig.json",
         pwd: currentProject?.path || "/Users/demo/project",
         "echo hello": "hello",
         whoami: "automaker-agent",