I can't figure how to, by default, exclude everything and only include
what I'm interested in.
If I've understood you correctly, I think it does in fact work the way you
want it to. Have you tried including the files you are working on and
leaving out the exclude?
include = 'src,test'
would only include the src and test directories without the need to exclude
anything. You could then exclude anything you didn't want within those
directions with your exclude.