text: Title: Use native config files for coverage, flake8, and yapf
  Body: The cookiecutter template puts the configuration for `coverage`, `flake8`, and `yapf` in `setup.cfg`.
  
  However, `setup.cfg` is traditionally the `setuptools` config file. `setuptools` traditionally provided `setuptools.config.read_configuration()`, but the project is abandoning `setup.cfg`, and the tool is deprecated.
  
  I haven't checked whether these specific tools have their own parsing or not. But, to avoid confusion or deprecation warnings (or ultimately errors), we should probably move the configuration for these tools to their own native config files.
  
  * coverage: https://coverage.readthedocs.io/en/6.4.4/config.html#configuration-reference; Note also https://pytest-cov.readthedocs.io/en/latest/config.html#caveats
  * flake8: https://flake8.pycqa.org/en/latest/user/configuration.html#configuration-locations
  * yapf supports several alternatives: https://github.com/google/yapf#formatting-style (I thought MolSSI advocated Black. Is yapf in use?)
  * https://docs.codecov.com/docs/codecov-yaml