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I know it's an old topic, but the problem still exists in 13.0sp1.
I've followed your solution, adding the appropriate files to the environmental path. The nios2-download command is now found, but new errors return:
/cygdrive/c/altera/13.0sp1/nios2eds/bin/nios2-download: line 2: $'\r': command not found.
/cygdrive/c/altera/13.0sp1/nios2eds/bin/nios2-download: line 4: $'\r': command not found.
/cygdrive/c/altera/13.0sp1/nios2eds/bin/nios2-download: line 15: $'\r': command not found.
/cygdrive/c/altera/13.0sp1/nios2eds/bin/nios2-download: line 17: $'\r': command not found.
/cygdrive/c/altera/13.0sp1/nios2eds/bin/nios2-download: line 23: $'\r': command not found.
/cygdrive/c/altera/13.0sp1/nios2eds/bin/nios2-download: line 25: $'\r': syntax error near unexpected token '$'{\R'''cygdrive/c/altera/13.0sp1/sp1/nios2eds/bin/nios2-download: line 25: '{
nois2-terminal: connected to hardware target using JTAG UART on cable
nois2-terminal: "USB-Blaster [USB-0]", device 1, instance 0
nois2-terminal: (Use the IDE stop button or Ctrl-C to terminate)
Now what :( this is so frustrating. I spend literally 12 hours not to get a demo working that was provided by altera. Shouldn't this be an out-of-the-box example?
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EDIT: ok, I finally solved the above problem by opening each file in sublime and changing the encoding.
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