Robert Woodruff’s departure as artistic director of Boston’s American Repertory Theatre will mark the end of an era when it occurs this summer. But as recently as last fall, Woodruff was certain he would be returning to ART, and the company’s board had no reason to think otherwise. But in the end, the decision came down to money: there was a strong sense on the board that Woodruff’s uncompromising stance on artistic matters was fiscally untenable, and he was told that his contract would not be renewed.