I would like to solve this problem but am not an autocrlf expert.
Me neither, but I can definitely see some inconsistencies in the repo when it comes to EOL. I downloaded few files directly bypassing git: $ wget -q --no-check-certificate https://github.com/ceki/logback/raw/master/logback-core/src/main/java/ch/qos... $ wget -q --no-check-certificate https://github.com/ceki/logback/raw/master/logback-core/src/main/java/ch/qos... $ file EnvUtil.java FileSize.java EnvUtil.java: ASCII English text, with CRLF line terminators FileSize.java: ASCII English text EnvUtil.java is one of the files being marked as modified after fresh clone, while FileSize.java is not. As for cloning, when I change my core.autocrlf setting either to false or to true, no modified files are shown after clone. Only /input/ causes problems - but this is a recommended Linux setting [1]; also for sure some files with CRLF leaked into the repository.
Once on a Windows on a Linux host, I cloned a fresh copy a did not notice the problem you describe. I had autocrlf = true. On the Linux machine, removing autocrlf did not seem to make any difference.
Can you try with autocrlf = true and with autocrlf unset?
Cheers,
pozdrowienia -- Tomasz Nurkiewicz http://nurkiewicz.blogspot.com