'''Answer''': This happens because the default setting for msys git on Windows is to checkout files with CRLF line endings. To fix this, you need to reinstall msys git and when you do, choose option 2 here http://help.github.com/images/bootcamp/bootcamp_1_win_install_7.jpg. Once you've reinstalled msys git, you need to checkout the repository with the correct LF line endings with the following commands: <pre>git ls-files -z && | xargs -0 rm ;git checkout .</pre>