I've been asking myself for a while how ATC can maintain air traffic safety with regard to military aircraft - or if they just don't.
As I understand it, all bigger planes (let's for now focus on commercial airliners) have mandatory transponders and warning systems like TCAS and similar. By usage of such systems, ATC knows their position, altitude, heading etc. which is used for planning of take-offs and landings just as well as air traffic safety. Also, systems like TCAS allow pilots to directly respond to unsafe situations even if ATC "didn't see it coming". In short, lots of regulations and techniques to make flying safe.
Now I know even less about military aircraft, but I do know they have transponders, too. I suppose, since enemies would have it a bit easy, those transponders don't operate the same way civil transponders do; or at least they use different frequencies, encryption and what-not. I don't know if they have TCAS but, I suppose, even that could possibly be exploited by enemies.
If I assume correctly, civil ATC cannot necessarily see military aircraft. I've read in another question that FAA doesn't have much power over military but that's just the US anyways. Also, the answer in yet another question suggests that military aircraft do not have to maintain separation.
So, what's the verdict? Do military aircraft assume civil regulations while not in "combat mode"? Or are civil ATC indeed oblivious of military air movements and the military has to provide safety by regulating military and watching civil traffic?