Fix: Ensure all skills are tracked as files, not submodules

skills/loki-mode/examples/todo-app-generated/frontend/src/main.tsx

@@ -0,0 +1,10 @@
+import React from 'react'
+import ReactDOM from 'react-dom/client'
+import App from './App.tsx'
+import './index.css'
+
+ReactDOM.createRoot(document.getElementById('root')!).render(
+  <React.StrictMode>
+    <App />
+  </React.StrictMode>,
+)