Villains go crazy here a lot with sets to get all the money in. When you raise to 31 and he shoves, I think its pretty obvious he has a small flush/set/2pair that wants to get it in now. Given this information your hand does pretty poorly here. Id probably call the 15 and proceed on turn card, his actions on turn may confirm your suspicions. 

I think I'd just call the flop check raise vs most people. A HUGE chunk of his flop check raise bluffing range is going to be Ahx and you holding that card in your hand makes it a ton more likely that you're running into either a flush or 2 pair + . Another upside to calling here is that a set likely won't be able to fold the turn (whether that be by bet calling or check calling) due to their redraw against your flushes and a made flush will likely call at least one more bet depending on how high a flush villain holds. So with that in mind, you're not only "chasing" to hit your hand expecting to get no more action when you hit. 

Maybe i am completely out of line but what about folding the flop? seems like we are looking for 9 or maybe 7 outs and what if we hit an ace? Maybe James are right about us getting good implicit odds on turn when we hit but i think our opponents with this raising size in general has 90-100% "nuts" and it feels like very many times we are going to call and then fold the turn very often?

I'm cbetting this flop with near 100% frequency [and i feel like most people are]

Do you mean cbetting 100% with this hand, right? Because this is a board where you should be giving up or pot controlling with many holdings.

does say .. A9ss play the hand this way? TT/JJ? a hand like KcQh?

Even if he plays like this, it would be only a small percentage of the time, so you can't stove these hands in his range without weighting the frequency. For argument sake, let's say his range has only 99-JJ, we can't put this range on pokerstove, because he will raise 100% of the time with sets and like 15% with TT-JJ.

That being said, I don't believe most villains would raise A9, TT-JJ at all. And certainly, it would be pretty odd to raise to this size.

This is the type of board that favors the caller, so a smaller bluff-raise would get the job done, so why is he raising so large? It looks really valueish to me.

For these reasons I would fold to his $15 raise, it's obvious exploitable to fold such a strong hand if you are cbetting a lot in this board, but I doubt the villain will raise enough hands to this size to explore us.