I have searched a lot and viewed a lot of answers with no luck. I am using Android Studio 1.5.
Here is what I have done:
- VCS > Import into Version Control > Create Git Repository...

- I created a directory "Git Repo".
- I selected the root "app" directory.
- VCS > Git > Checkin Directory...

- I receive Nothing to Commit (No changes detected).

- I modified one file. I still receive Nothing to Commit.
This is one of the times where 3 hours are wasted by an IDE.