OK, looks really really good now, nice work;

I'd suggest one last thing: whichever is a binary that is the most indicative one (and ends up in $PATH), should rather be under files with an entry, eg. `bin/cd-hit`; this is a good catch step to verify compilation actually did the task.

In retrospect, it may be even possible to be fed by `files_to_copy`, which is even nicer.

Once done, ready to merge!