flake8: fix flim-omero
flake8: fix omero_web_iis

* flake8 fixed but windows line endings left in
* two comment lines marked as noqa to preserve urls
flake8: fix runProcessor
flake8: fix runTables
flake8: fix shellserver
flake8: mark import-only file model/init as noqa
flake8: update config in include fixed files
Merge pull request #3043 from ximenesuk/flake8-omero-various-2

Flake8 various files under OmeroPy (part 2)