I have been bitten by the Windows/Linux line-ending issue with git. It seems, via GitHub, MSysGit, and other sources, that the best solution is to have your local repos set
Follow these steps if none of other answers works for you:
git config --global core.autocrlf true; if you are on Unix, do git config core.autocrlf inputgit rm --cached -r ..gitattributesgit add -Agit reset --hardThen your local should be clean now.