GitHub - estragou completamente os ficheiros locais do gitHub no meu computador

Criei um repo na pasta errada. Ou seja, a pasta Utilizador no SO onde todas as pastas do utilizador são de imagens, vídeos a documentos. Assim, empurrei tudo isso para o gitHub sem saber e agora já não posso criar um repo porque os ficheiros com que trabalho estão na pasta de documentos, que está dentro da Pasta de Utilizador. E isso implicará que estou a criar uma repo dentro de uma repo. Assim, quando vou para o terminal e corro o estado de idiota, isso mostra-me isto:

# 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")

Escusado será dizer que nunca sou capaz de puxar nada. Diz que tudo está em dia. A certa altura, tive um repo que carregou essas pastas sem os ficheiros para o gitHub, mas apaguei isso.

Alguma sugestão?