Payment server

That's the right way to do it as riX says.  The software can generate a new bitcoin address whenever you need one for each payment.  "Please send X bc to [single-use bitcoin address] to complete your order"  When the server receives that amount to the bitcoin address, that could trigger it to automatically fulfil the order or e-mail the shop owner.

Adding command line support is a high priority.  It's just a matter of getting the time to code it.