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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.

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Uhm, so you had done a push to github, and that failed. You wiped out the local repo, then you did a pull, doesn't that mean you got that half-uploaded repo from the first step? Anyway, talk to the sysadmin, they should have a backup. I kinda think you are screwed. In the future, don't make changes to the production system until you have tested it on a dev system, or at least a dev directory. –  Zoredache May 2 '13 at 6:41
    
But the repo on github is empty! –  David May 2 '13 at 6:43
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Is the repo public? What is the URL? In any case, you have data loss. Find the sysadmin. I really have no idea what you have done to your data. I doubt any of us here can magically make your data re-appear, but your system administrator might be able to do that. –  Zoredache May 2 '13 at 6:43
    
Private repo... –  David May 2 '13 at 6:45
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The fact that the server is an apache server makes absolutely no difference. Zoredache is right, you have lost data and you need data recovery or a backup. –  ohope5 May 2 '13 at 7:08

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