git rm --cached -r .
# Remove everything from the index.
git reset --hard
# Write both the index and working directory from git's database.
git add .
# Prepare to make a commit by staging all the files that will get normalized.
# This is your chance to inspect which files were never normalized. You should
# get lots of messages like: "warning: CRLF will be replaced by LF in file."
git commit -m "Normalize line endings"