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# From the root of your repository remove everything from the index
git rm --cached -r .

# Change the autocrlf setting of the repository (you may want 
#  to use true on windows):
git config core.autocrlf input

# 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 "Fixed crlf issue"