Remove old integration test now handled with Aruba

These no longer need to be maintained because we now have a more
thorough integration test through Aruba. Additionally, we can now
restructure the code without having to account for these tests.
Re-write empty directory tagging to use Find

Find is a module in the stdlib which will talk through a directory tree.
The code will now flag empty hidden directories in a repository while
correctly ignoring the .git directories. (The tests has also been
updated to validate this.)

Additionally, I also added a test helper method for creating directories
in the local testing repository.