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With synchronized projects, files that originate on Windows machines seem to acquire windows line termination characters, even if the files were originally linux/unix files, and are being synchronized to linux systems.
This should be easy to fix by setting core.autocrlf to true. As a temporary workaround this should even be possible to do manually. Set it in .ptp-sync/config on the Windows machine.
I hesitate to add this flag, because it can possibly corrupt files. Also, Eclipse provides an easy way to deal with line endings, which I just discovered: http://stackoverflow.com/questions/1886185/eclipse-and-windows-newlines
Should this be closed then?