Gigabit Ethernet Interface (via Marvell 88E1111) with Cyclone IVE FPGA

It needs to be echo $PATH with capital letters, environment variables are case sensitive.

And what happens if you type nios2-app-generate-makefile in the Nios II command shell? Do you also have the command not found, or something like "SEVERE missing required command line option" ? (if it is the latter, then it means that your cygwin installation is ok)