Migration Cleanup

This release was prompted by the migration of our application to a new server, which led to a broader cleanup of configuration, processing scripts, and infrastructure.

• Unified Docker Compose setup (prod, prod.local, dev)
• Renamed Docker files, services, and containers for clarity.
• Centralized environment variable handling in Compose files.
• Simplified backup and logging (moved to central handling).
• Updated input and reannotation processing scripts + example data.
• Minor UI tweaks
• Cleaned and restructured README
Breaking Changes
• Environment variables and Compose files have changed → update .env and use new Compose configs.
• Some backup and logging scripts removed → rely on central handling.