Is there any way to do differential copies of a directory from Windows to Linux over ssh, sftp, scp, or similar? Preferably not rsync since they are all cygwin based and force you to use the /cygdrive/c/... file path convention which is a pain. I'm trying to frequently upload new code to a Raspberry Pi and have been using pscp but it doesn't allow differential copies or excluding directories/files, as far as I can tell.
Unison is a well-established, open-source tool for this. It has pre-compiled binaries for Linux, native Windows, and Cygwin.
I personnaly use WinSCP to make this. It's pretty easy to script or use graphically.