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To reproduce, create a new project with the following 4 files: none.txt = "" unix.txt = "\n" windows.txt = "\r\n" mac.txt = "\r" Diff considers all 4 files equal (0/0 differences). In my opinion, when "Ignore Leading And Trailing Whitespace" is unchecked in the Diff options, this case should be detected. If you add the above files to a Git repository & then rename the files (none.txt becomes unix.txt, unix.txt becomes windows.txt, ...), git will show all 4 files have changed, but when doing "Diff to HEAD" NetBeans says there are no differences. In my opinion, this is confusing at least.