Move setup.cfg to the top-level directory

This commit migrates the `setup.cfg` configuratoin file to the root directory. Validation of the Python files can be performed with the following command ( used in the Travis Python build):

```
flake8 -v .
```

Some minor sub-folders/files are modified to comply with `flake8` as part of this PR.

The non-`flake8` compliant files under `docs/hudson` are simply removed since the logic is either irrelevant (SVN) or has been moved to `omego`.

/cc @ximenesuk 

--no-rebase