Melt the stick of butter in a large pot over medium heat. Add the onions, garlic, bay leaves, thyme, salt and pepper and cook unti the onions are very soft and caramelized, about 1 hour. Add the wine, bring to a boil, reduce the heat and simmer until the wine has evaporated and the onions are dry, about 5-10 minutes. Discard the bay leaves, thyme sprigs, and garlic cloves. Dust the onions with the flour and give them a stir. Turn the heat down to medium low so the flour doesn't burn, and cook for 10 minutes to cook out the raw flour taste. Now add the beef broth, bring the soup back to a simmer and cook for 10 minutes. Season, to taste, with salt and pepper.

Preheat oven to 400°. Cube ciabatta bread into 1 1/2-in chunks. Toast bread in 400° oven for 5 - 10 minutes, turning chunks once halfway through. Ladle soup into oven-proof bowls or ramekins. Divide the toasted croutons among the bowls. Top each with slices of fontina cheese. Place under the broiler, until the cheese is golden and bubbly, being careful not to burn cheese. Serve immediately.