GitHub suggests that you should make sure to only use \n as a newline character in git-handled repos. There’s an option to auto-convert:
$ git config --global core.autocrlf true
Of course, this is said to convert crlf to lf, while you want to convert cr to lf. I hope this still works …
And then convert your files:
# Remove everything from the index
$ git rm --cached -r .
# Re-add all the deleted files to the index
# You should get lots of messages like: "warning: CRLF will be replaced by LF in <file>."
$ git diff --cached --name-only -z | xargs -0 git add
# Commit
$ git commit -m "Fix CRLF"
core.autocrlf is described on the man page.