Add migration for commands->prompts, warn about deprecated hooks/tools dirs

- Auto-migrate commands/ to prompts/ on startup
- Warn if hooks/ or tools/ directories contain custom extensions
- Show deprecation warnings in interactive mode with keypress to continue
- Update CHANGELOG and docs with full migration guide

README.md

@@ -63,6 +63,11 @@ cd packages/coding-agent && npx tsx src/cli.ts
 cd packages/pods && npx tsx src/cli.ts
 ```
 
+To run tests that don't require an LLM endpoint:
+```bash
+./test.sh
+```
+
 ### Versioning (Lockstep)
 
 **All packages MUST always have the same version number.** Use these commands to bump versions: