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

skills/loki-mode/examples/todo-app-generated/PRD.md

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+# PRD: Simple Todo App
+
+## Overview
+A minimal todo application for testing Loki Mode with a simple, well-defined scope.
+
+## Target Users
+Individual users who want a simple way to track tasks.
+
+## Features
+
+### MVP Features
+1. **Add Todo** - Users can add a new todo item with a title
+2. **View Todos** - Display list of all todos
+3. **Complete Todo** - Mark a todo as done
+4. **Delete Todo** - Remove a todo from the list
+
+### Tech Stack (Suggested)
+- Frontend: React + TypeScript
+- Backend: Node.js + Express
+- Database: SQLite (local file)
+- No deployment (local testing only)
+
+## Acceptance Criteria
+
+### Add Todo
+- [ ] Input field for todo title
+- [ ] Submit button
+- [ ] New todo appears in list
+- [ ] Input clears after submit
+
+### View Todos
+- [ ] Shows all todos in a list
+- [ ] Shows completion status
+- [ ] Empty state when no todos
+
+### Complete Todo
+- [ ] Checkbox or button to mark complete
+- [ ] Visual indicator for completed items
+- [ ] Persists after refresh
+
+### Delete Todo
+- [ ] Delete button on each todo
+- [ ] Confirmation before delete
+- [ ] Removes from list and database
+
+## Out of Scope
+- User authentication
+- Due dates
+- Categories/tags
+- Mobile app
+- Cloud deployment
+
+## Success Metrics
+- All features functional
+- Tests passing
+- No console errors
+
+---
+
+**Purpose:** This PRD is intentionally simple to allow quick testing of Loki Mode's core functionality without waiting for complex builds or deployments.