Ok, now this is just weird to me.
If I run the Inspection on the Whole Project, it does JUST the project files (module), but if if I create a Scope that excludes a couple of files, then the Inspection runs on the Project AND all included folders (includes), which is BAD (it will never finish, those are PEAR files and other 3rd party extensions.)
Why does it do that? If that is designed behavior, why don't those folders show up in the Tree on the Scope creation page? How do I exclude those (can I exclude the entire include folders)?