Fix Windows PyWinPTY terminal boundary string drops via bat spool execution and full Windows deployment support

Refactor configuration flow (Day 0 vs Day 1 separation) and add startup scripts ...

- Stop AI provider settings from syncing back to config.yaml (stored in DB only now).
- Parameterize frontend port in docker-compose.
- Add start_server.sh and stop_server.sh scripts.
- Update .gitignore to exclude scratch files.