[Fix #1425] Find included files in a simpler way

Only look in the "base" configuration when finding the target files, not in the configuration associated with each file under consideration. This removes a feature that has existed for a long time, but hopefully isn't used by many people (the ability to have `AllCops/Include` parameters in `.rubocop.yml` files in subdirectories). We didn't cover the existing behavior in specs, but the new behavior is covered.

Also includes an optimization (the use of `Set` in `TargetFinder#target_files_in_dir`) that's aimed at #1427. I've measured a 3 fold speed increase for the file finding phase when I had a hidden directory containing 12000 files. Down to 6s from the original 18s.