Fix flake8 no-op run in CI and clean up resulting failures

The CI runs this flake8 command:

flake8 --select=F */python */options

It's supposed to check for things like references to undefined variables and unused imports.

But the globs */python and */options don't match any folders in the Moore repo root, so the command runs over no files! We should fix the command to actually process all of our Python files.

But there will be some clean-up to do, as all the files are now un-linted 😅

$ flake8 --select=F **/python **/options | wc -l
1745