I am not sure what is more the issue. That the mutant generation only copies over python files or that the also_copy command overwrites the mutants since it runs afterwards.

Basically I have a repo with a bunch of schema definitions in JSON files and a few other files in the source directory. These files need to be present for the tests to run but when doing mutmut run it doesn't copy the files over since it only looks for python source files when copying them into the mutant folder and the tests fail.

I could specify the dozens of schema files into also_copy but that is extremely tedious and prone to failure anytime a filename is changed or a new file is added.

I think the solution would be to copy over the entire source directory then make the mutants and overwrite the source files with the new mutated files instead. I think that would solve both issues I am running into and just be a more resilient option. The also_copy config option could still exist to make sure files outside the source dir are included but only copying python source files is limiting.