Harmonize python tool configuration

[tmadlener]

Currently we have a .flake8, a setup.cfg and a pyproject.toml with partially contradictory settings. These should all be in one place only and consistent.

[m-fila]

How about going with ruff?

[tmadlener]

Yeah probably a good idea to simply switch everything over to that to be consistent with the rest of Key4hep.