In the same downloaded file you get a command-line ISP programer, is explained in the manual (as is logic).
With this program you can do ISP automatic or add serial numbers etc.
You can't do ISP directly with a terminal program.

I usually use the batchisp instead flip because is faster and you can configure all the parametres, chanel, speed, device type etc. So i have a buton in my ascii editor for assambling and other for programing via ISP, so i can do all with two clicks.

Félix.