Extend usage of configuration file

[JasperCraeghs]

Maybe a side note, what if we would add the code-quality field in config json file as well - then there would not be a case where we would have to be careful about the code-quality flags placement (or ignore-retval, include-sphinx-deprecation, name, etc?). Probably this is then more of a feature request if we decide to go this way...

Originally posted by @Letme in #131 (comment)