Move external files to omero_ext

As part of the effort to have all files under `OmeroPy` pass `flake8` this PR moves three external files that should not be modified under `omero_ext`. Files importing the moved files have been adjusted so functionality should not be affected and integration tests should continue to pass.

--no-rebase

Initial excluded as the changes to configuration will  conflict with other open PRs.

--exclude

/cc @sbesson