Updated flake8 dependency, added autoflake

[Bartvaderkin]

The flake8 dependency was ancient and needed to update so we can use autoflake

With autoflake you can automatically fix some flake8 issues, so it works similar to black and isort.

I use this mostly for unused imports, because I always forget:

autoflake --in-place --remove-all-unused-imports

(also fixed some issues from new tooling)