The module linter currently flags empty files in the snapshot, meaning that for those files I have to check the name only (I guess). Wouldnt it be kind of important to know if a file that was empty stops being emtpy?

Nope, you should not have empty files except in stubs.

Hmm, what's the reasoning here? If a real tool test generates e.g.

errors.log

or

unassigned_seqs.txt

or some such, which under normal circumstances is empty, but could feasibly have content even with a successful exit code, isn't it right that we want to check that a new version or change isn't producing some new output?

That is basically why I thought about this, I updated a tool that creates a file named

pairing_issues

which is empty, but it seems like it would be good to know if pairing issues start appearing

Good point. How about you write a snapshot of the content making sure it stays empty?