None of the Avengers know if [any ship] are together. They can't get a straight answer because the couple isn't sure either.
It's getting hard to ignore, really. There seems to be a lot of unusual activity within the Avengers and SHIELD lately: unusual visits from Asgard; even-more-cramped-than-usual movie nights; challenges to duels being thrown down over breakfast; and Fury doesn't seem to be as intimidating as normal.
They're all sitting around the kitchen table talking about how much they've still seen Pepper around even though she and Tony split up a few months back. Clint comes to the logical conclusion that she must be seeing someone else, since she's spending a lot of time not around Tony while she's there.
He volunteers Natasha to ask, but instead of getting an answer, she ends up going out for cocktails with Pepper and Sif. When she reports back at the end of the evening, the best she has for anyone is, "I'm pretty sure they're really into each other, but even they're not quite sure what's going on."
It gets worse when Darcy drunkenly confesses to Clint that she's pretty sure that she walked in on Thor and Tony in the bathroom a few days ago and now that image is burned into her retinas, and could someone please tell them to lock the door if they're going to do that? He sighs and stages an intervention with Tony and Thor, who both seem to be really into denial about the whole thing.
Everyone thinks that JARVIS secretly has a thing about the Iron Man suit, especially when he carefully side-steps the question when Tony pointedly asks him about it. JARVIS gets irritated, as much as an AI can, when Tony takes out the new suits before everything has been tested and especially when he brings them back scratched or destroyed. They're not sure if JARVIS is just over-protective of all of the AI, or if it's something else, but there's no way to know for sure.
Steve is even more nervous around Natasha than Bruce is around Darcy, which tips them all off that something might be going on there, but Natasha doesn't kiss and tell. Clint can't get a direct answer, and he decides it's because she doesn't know, either. He's starting to think that the only ones of them who actually know their own personal relationship status are Phil and himself, and even that's not quite a sure thing. (Clint has been very patient, but he's almost to the point of showing up naked in Phil's office to get this thing rolling.)
Phil accidentally catches Director Fury and Agent Hill in what could be a compromising position, until he sees Hill flip Fury over her shoulder and onto the floor on his back. She offers a hand to pull him up, but he knocks her off her feet, and Phil leaves before he has the chance to see something he'll really regret.
Bruce takes Darcy a cup of tea one night when she's out on the balcony, staring out over everything. She kisses his cheek, and he stays out there with her, one arm resting loosely around her. Thor gets a misty look in his eyes when he sees them, and he can't bring himself to interrupt their moment to ask if this is official.
Clint is pretty sure they've all finally admitted to themselves and each other who's involved with who by the time he finally pushes enough buttons to find himself bent over the desk in Coulson's quarters in the tower.
He can't say he regrets going the long way around.