Make the filling: Preheat oven to 300 degrees. Season short ribs with salt and pepper. Dredge short ribs in flour, coating all sides. Transfer to a large plate. Heat oil in a large Dutch oven over high heat. Working in batches, brown short ribs, about 1 minute per side. Transfer to a large plate using kitchen tongs.
Reduce heat to medium. Add yellow onion to Dutch oven, and cook until golden, about 8 minutes. Add garlic. Cook for 2 minutes. Return meat to Dutch oven. Add stout and rosemary. Bring to a simmer. Cover, and transfer to oven. Bake for 2 1/2 hours.
Remove Dutch oven from oven, and add cipollini onions. Braise until meat is tender and onions are cooked through, about 30 minutes. Shred meat using 2 forks. Season with salt and pepper. Divide filling among eight mini (1-cup) pie plates, or transfer to a 12-inch (8-cup) gratin dish.
Make the topping: Raise oven temperature to 375 degrees. Peel potatoes, and very thinly slice each (preferably on a mandoline). Arrange potatoes over meat to form tight concentric circles, working around the edge and overlapping each potato by three-quarters. Brush with oil, and sprinkle with salt and pepper. Bake until topping is golden and filling is bubbling, about 45 minutes for mini potpies (1 hour for large potpie).