With Git, when using the autocrlf = true flag, a warning is still given when line-endings are changed.
autocrlf = true
I understand what the warning is for, and how to
You should use core.autocrlf input and core.eol input. Or just don't let git change the line endings at all with autocrlf false and get rid of highlighting of crlfs in diffs, etc with core.whitespace cr-at-eol.
core.autocrlf input
core.eol input
autocrlf false
core.whitespace cr-at-eol
Hope this helps