The command 'alias' rewrites the configuration file completely when a new alias is added. The default file is 'setup.cfg'. All comments of the original file are stripped off before, though the new 'setup.cfg' does not contain any comments.

The comments should be kept literally, just the section '[aliases]' should be modified.

The comments in the section '[aliases]' should be basically kept, even though a manual modification by the user could cause problems e.g. in case of deleting an alias by the 'setup.py alias' command.

Anyhow, at least the only section modified should - must - be the '[aliases]' section.

Even though this involves 'setuptools', I write this issue here because of the tight coupling of 'distutils' and 'setuptools' e.g. by the passed 'self' parameter.

I have tested 3.8.0, but as far as I can see this is the case for all releases.