[barsikjal]

OK, are we taking this in the context of strict construction?

I guess, although I don't believe any sort of "construction" rule needs to be applied. It's unmistakably clear -- the President is the Commander in Chief of the military. Thus, the decisions about how the military carries out its war-making function are his, not the Judiciary's. The conduct of armed hostilities including the identification, capture and detention of enemy combatants are military functions.

If so, who are we at war with? AQ and the Taliban are nebulous entities at best. I gather your question may be based on the false premise that the country must be in a declared state of war for the Commander-in-Chief power to apply. If so, this is simply incorrect; you'll see that no such proviso is attached to that grant of power.

But to answer your question ... No more so than any other enemy. They often disguise themselves as civilians and conduct sneak attacks (mostly in violation of the laws of war, by the way), which may make identifying and taking them out of the fight more challenging. But this does not change the fact that this role is reserved to the President as Commander in Chief (and his designees, of course), not the Judiciary.