http://www.rtuin.nl/2013/02/how-to-make-git-ignore-different-line-endings/
echo "* -crlf" > .gitattributes
Do this on a separate commit or git might still see whole files as modified when you make a single change (depending on if you have changed autocrlf option)
This one really works. Git will respect the line endings in mixed line ending projects and not warning you about them.