Add checks for commit count on nothing scenarios

This was being checked in the other scenarios, but not in the nothing.
I have added these in relation to trying to debug #77 but as they pass
without codes changes, this is not the problem that is being seen.
Fix missing hidden files in empty directories

Dir.glob was being used such that hidden files where getting ignored
when checking for empty directories. This resulted in the .gitignore
marker files getting added repeatedly creating more churn in the change
notifications.

I think that this will help to address #77, but there is still more
unnecessary change activity to investigate.
Merge pull request #78 from acant/bug/extra_file_changes

Working on removing the extra file changes and extra notifications