What to do with the prisoners currently held in Guantanamo? Or others we might capture amid a war without borders or fronts? “Prisoner of war” has very clear definitions according to the Geneva conventions. And yes, it can apply to irregular forces, even those that do not represent an official nation state.
Calling the violent men in Guantanamo "POWs "does not mean they can be tortured. In fact, the opposite. They must be treated according to Geneva protocols. But it does mean they can be held indefinitely, in a military facility on American soil, so long as hostilities continue in a plausible state of war. Moreover, there is no ticking clock to bring charges against them -- in fact, filing charges against such men might be illegal, if their actions were against even somewhat legitimate military targets. Certainly there is no requirement to mix them with the regular population of a federal penitentiary. In fact, that too violates Geneva.