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In the Cygwin environment the native Windows serial COM# ports get mapped to /dev/ttyS# for POSIX compatibility. While # is one number lower inside the environment than the COM port number because it's 0 indexed instead of 1. I added the necessary handling to all the dependent parts I found which allows uploading to /dev/ttyS# when the cygwin platform is detected. Now the usual "make px4fmu-v4 upload" and "./Tools/upload.sh build/px4fmu-v4_default/px4fmu-v4_default.px4" work.