How to generate .jbc file from command line?

Thank you for your reply FvM.

I'm not sure how or if this deals with multi device chains though? There is nowhere I can see to define this in the device options. This is why I want to use a .cdf file where I've then specified the devices in the chain and which one I wish to program.

However I have also just received a response from Altera that tells me to use the following command which works and produces an identical .jbc output file :

quartus_cpf -c top_level.cdf output.jbc