Problem
I added and pushed a bunch of files into my repository, but now I need to put it into a subfolder.
Solution
Git is smart and will find the files you moved. Do the following:
$ mkdir newFolder
$ mv oldFolder newFolder
$ git rm -r oldFolder
$ git add newFolder
source: http://stackoverflow.com/questions/3900805/git-command-to-move-a-folder-inside-another
keywords: git move files to another folder