Preheat the oven to 450 degrees F. Season the short ribs with salt and pepper. Dredge in flour, shaking off excess. Reserve the flour. Heat the oil in a large skillet over medium-high heat. Brown the short ribs on all sides, and then transfer to a casserole. Roast short ribs 30 minutes. While this occurs, cook the onions and garlic until tender, about 5 minutes, in the skillet used for the short ribs. Mix in the thyme and 3 Tbsp of the reserved flour; discard the rest. Slowly pour in, mixing steadily, the stock. Bring to a boil, and then season with salt and pepper and reserve on low heat. When the short ribs have roasted 30 minutes remove from the oven and drain away the excess fat. Reduce the oven temperature to 325 degrees F. Pour onion/garlic mixture over the ribs. Cover and bake for 1 1/2-2 hours, or until the meat is very tender and falling off the bone. Skim any fat from the surface of the ribs before serving.