Refactor backend into a reliable modular monolith

[simajkeee]

Summary

Refactors the FastAPI backend into clear HTTP, application, persistence, storage, and background-processing boundaries while preserving the public API contract.

What changed

• Split HTTP routes into api/files.py and api/alerts.py.
• Added request-scoped dependency assembly and centralized domain-error handlers.
• Extracted file and alert repositories from application workflows.
• Added FileService and ProcessingService use cases.
• Moved filesystem access into FileStorage.
• Added streamed uploads, temporary-file cleanup, atomic promotion, and DB-failure compensation.
• Replaced the three-step Celery chain with one process_file task.
• Created the worker async engine/session factory in the worker event loop.
• Added row locking, terminal-state guards, and alert de-duplication for retry-safe processing.
• Added query indexes for file and alert list/FK queries.

Verification

uv run ruff check src tests migrations
env -u POSTGRES_USER -u POSTGRES_PASSWORD -u POSTGRES_DB -u POSTGRES_HOST -u PGPORT uv run pytest
POSTGRES_HOST=localhost uv run alembic upgrade head