Place flour and pepper in a plastic bag. Add beef pieces, a few at a time, shaking to coat. In a 4- or 6-quart Dutch oven brown half of the beef in 1 tablespoon of the hot oil; remove beef. Add remaining oil, remaining beef, onion, and garlic to Dutch oven. Cook until beef is brown and onion is tender. Drain fat, if necessary. Stir in wine, scraping until the brown bits are dissolved. Return all beef to Dutch oven. Stir in beans, broth, tomato, and dried thyme (if using). Bring to boiling; reduce heat.