I am in australia and this is my university's website server. I wanted to add the files to git. So I created a repo in github and then on my server did a git clone of the repo, add *, committed and pushed.
The website was huge and after some time it gave an error saying that repo was too big. I removed some files, then realized git would store previous files too and the error will still be there.
I then removed the .git folder and again this time, did a git init and then git remote add origin. I did a git pull to get that README.md file which github creates and now boom! half the files in the repo disappeared. Please help me now as I'll be screwed if they find out. It is an apache web server.