I have been using Intellij IDEA w/git integration for Android dev for sometime. I have recently upgraded to Android Studio (v0.1.1) and now one of my favorite shortcuts Ctrl
I had the same problem. At the first place you initialize git and add files for tracking, some files asked to add to git. when you ignore it and check "do not ask / remember" they add to .gitignore
file.
just open .gitignore
file and check if the specific folder is included so remove it and the gray color of folder and files will change to red and you can add them simply.
hope work for you