Resolve "Migrate SQLAlchemy mappings to 2.0 format"

Description

Changed to version 2-style mappings (not for migration base).

Fixed a lot of resulting mypy errors. The remaining mypy errors should be handled with #2237 (closed).

Added a standalone test to test if migration script is up to date.

Notes to review (code/docs/QA)

Related issues

Closes #2236 (closed)