Why Android Studio delete all the files on git commit?

Why Android Studio delete all the files on git commit?

I recently migrated from Eclipse to Android Studio. Now I have all my
project working but directory structure has changed in Android Studio so I
have to commit this changes to my GitHub repository so I did:
Copied .git folder from Eclipse Project to Android Studio Project
VCS -> Git -> Add to VCS
So now I have a my Git repository and I can see all the changes I did in
Eclipse in Changes View. Now to commit the new project structure:
VCS -> Commit Changes
A new windows is opened with the changes and I see Android Studio want to
delete ALL my files except 2, one I modified on Android Studio and the
other a .iml file.

So when I commit all the files of my project are deleted from my git
repository instead of committing almost everything and delete some folders
due to directory structure change . Why this happens? Is it a bug? Is
there any workaround?