Preheat the oven to 325 degrees . Season the short ribs with salt and pepper. In a large Dutch oven, heat 1 tablespoon olive oil over medium-high heat. Working in 2 batches, add the short ribs and brown on all sides, about 10 minutes total. Transfer to a bowl. Increase the heat to high, add the wine and bring to a boil. Lower the heat and boil gently until reduced by half, about 10 minutes. Return the ribs with any juices to the Dutch oven. Cover and bake for 1 hour and 15 minutes.
Meanwhile, in a large nonstick skillet, heat the remaining 1 tablespoon olive oil over medium-high heat. Add the onions, rosemary, and salt and pepper to taste; cook, stirring occasionally, until the onions begin to brown, about 5 minutes. Add the onions to the short ribs, cover and bake for 30 minutes longer.
Transfer the ribs and onions to a bowl. Let the cooking liquid stand for a few minutes to allow the fat to separate; discard the fat. Bring the liquid to a boil, whisk in the mustard and season to taste with salt and pepper. Add the tomatoes and return the short ribs and onions to the pot. Cover, lower the heat to medium and simmer until the tomatoes are tender, about 10 minutes.