Replace flake8 & isort with ruff (#3103)

Fixes #3101

- Remove `make sort` and `make sort-fix` make targerts
- Use `make lint` and `make lint-fix` instead.
- Make use of GitHub Annotation to surface issues as annotations
directly in the files changed, similar to CodeQL.
- Move stuff from `setup.cfg` to `pyproject.toml`
- Fixed the potentially buggy code. Each of the fix types is in
individual commits.