Remove excess fat from casserole, but leave a film of fat to cook vegetables. Return to burner over moderate heat. Stir onion, leek, carrots, celery, shallot, and garlic into casserole, if necessary adding more butter to coat. Raise heat to moderately high, add thyme and bay leaf and cook 4 minutes more, stirring frequently until vegetables are softened and tomatoes render juices.
Return shanks to casserole.
Pour on stock and wine, if necessary adding more liquid to cover ingredients. Bring to a simmer on top of stove, then cover and set in preheated 350 F oven. Shanks are done when meat is tender if pierced with a fork and can be pulled cleanly away from bone. Strain contents of casserole into clean saucepan, pressing on ingredients to extract all liquid and discarding solids. Using a ladle, skim any visible fat off surface of liquid.