Chris Duffy will have surgery to repair "wear and tear" on his rotator cuff. Obviously, he won't play again this season, although he could be ready for Spring Training.
If my math is right, Duffy isn't eligible for arbitration next year, so my guess is that he'll be back, but not in a starting role. He's too valuable to cut, and now he's too injured to trade. So my guess is that he'll be the Pirates' fourth outfielder next year unless Nate McLouth crumbles, and we'll see Duffy mostly as a defensive replacement and pinch runner. That's the role for which he's best suited anyway. The Bucs might hope he racks up a lot of steals in that role, then try to trade him to a contender if Andrew McCutchen is ready at midseason. (However, I wouldn't count on McCutchen being ready by midseason. He could actually probably use some time at Class AA next year - not that he'll get it.)