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

Question

I created a repo in the wrong folder. Meaning the User folder in OS where all the user folders are from pics, videos to documents. So I pushed that all to gitHub without knowing and now I can't create a repo anymore because the files that I work with are in the documents folder, which is inside the User Folder. And it will imply that I'm creating a repo within a repo. So when I go to terminal and I run git status, it shows me this:

# On branch master
# Your branch and 'origin/master' have diverged,
# and have 2 and 4 different commits each, respectively.
#
# Changes not staged for commit:
#   (use "git add/rm <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#   deleted:    Documents/m3/m3---Best-Game-Ever
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/CCLab_2/cclab_sketch_1/src/Boxes.cpp
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/CCLab_2/cclab_sketch_1/src/Boxes.h
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/ball_bouncing/Ball.cpp
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/ball_bouncing/Ball.h
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/bouncing_ball_classes/src/ball.cpp
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/bouncing_ball_classes/src/ball.h
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/ms_final/src/backGround.cpp
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/ms_final/src/backGround.h
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/ms_final/src/backGround2.cpp
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/ms_final/src/backGround2.h
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/mySketch/src/backGround.cpp
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/mySketch/src/backGround.h
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/mySketch/src/backGround2.cpp
#   deleted:    Documents/of_v0072_osx_release/apps/myApps/mySketch/src/backGround2.h
#   deleted:    README.md
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#   .Trash/
#   .bash_history
#   .dropbox/
#   .openmdao/
#   .ssh/
#   Documents/2nd_semester/
#   Documents/Arduino/
#   Documents/OpenMDAO/
#   Documents/Personal/
#   Documents/T.A/
#   Documents/gitHub/
#   Documents/mySite/
#   Documents/openFrameworks/
#   Documents/resources/
#   Documents/webcam-pulse-detector-master/
#   Dropbox/
#   Library/
#   Music/
no changes added to commit (use "git add" and/or "git commit -a")

Needless to say I'm never able to pull anything. It says that everything is up to date. At certain point I had a repo that uploaded those folders without the files to gitHub but I deleted that.

Any suggestions?

Answer 1

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 

Answer 2

T delete the .git folder in mac os recursively, go to the root folder of your project which contains .git folder and use:

find . | grep .git | xargs rm -rf

to remove its contents and itself.