GitHub - completely messed up the local files of gitHub in my computer

First things first:

1. Delete the Github remote repository where you uploaded your user folder (you don't want this to be public)

2. Delete the local repository in your user folder.

   # Be careful, dangerous command, it will erase your repository 
   # Make sure that you run this from the right folder 
   rm -rf .git
   

Now, if your local repositories bellow Documents start working again you are done. Else, delete and clone each one of them, one by one (of course that this will discard both uncommitted changes and commits that you have not previously pushed).

 cd ~/Documents/gitHub/
 # example, and again, be careful, it will erase your entire folder
 rm -rf repositoryA
 git clone git://github.com/myUser/repositoryA.git
 rm -rf repositoryB
 git clone git://github.com/myUser/repositoryB.git 
 # And so on