Working on removing the extra file changes and extra notifications

I hope that this PR will help to address #77 and the file churn and the extra notify activity that @quite is seeing with 0.5-pre3. The problems that I have seen so far:
* .gitignore files in empty directories were getting written over and over again (fixed)
* index is getting written unnecessarily

Starting the PR so that everyone else can see what I have so far. I'll be looking into how the check the index writes in the test next.