Git status shows files as changed even though contents are the same
I have resolved this problem using following steps
Remove every file from Git's index.
git rm --cached -r .Rewrite the Git index to pick up all the new line endings.
git reset --hard
Note that step 2 may remove your local changes. Solution was part of steps described on git site https://help.github.com/articles/dealing-with-line-endings/
Have you changed the mode of the files?
I did it on my machine and the local dev machine had 777 given to all the files whereas the repo had 755 which showed every file as modified. I did git diff and it showed the old mode and new mode are different.
If that is the problem then you can easily ignore them by
git config core.filemode false
Cheers