Cook down onions, stirring occasionally until soft and caramelized (about 30-40 minutes). Remove the bay leaves and thyme sprigs.
Sprinkle the onions with flour and cook another 10 minutes to cook the flour.
Add the beef broth and simmer for 10 minutes.
Place oven proof bowls on a large baking sheet and ladle the soup into the bowls. Top each with a slice of bread and cheese. Broil for 2-4 minutes or until cheese is melted. Serve.