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Move mypy and flake8 config to setup.cfg

@mfossati @cparle

This fixes bug:

mypy config is ignored when declared in tox.ini. This change introduces a setup.cfg to declare configs. While not directly affected, but for consistency reasons, I moved flake8 in there too.

Introducing setup.cfg was a change already planned, and will be adopted in the cookiecutter and existing projects.

@fab knowledge-gaps has the same issue (mypy conf declared in tox.ini).

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