Flake8 top-level OmeroWeb components

This PR flake8 all files at the top-level directory of `OmeroWeb` including `settings.py` and removes these files from the exclude list under `setup.cfg`

/cc @aleksandra-tarkowska @will-moore @ximenesuk @knabar 
That looks a bit odd despite being correct, does it work with the second line indented?