Melt the butter in a large Dutch oven over medium heat. Add the onions, garlic, thyme, and salt and pepper and cook until the onions are very soft and caramelized, about 30 minutes. Add the wine, bring to a boil, reduce the heat and simmer until the wine has evaporated, about 5 minutes. 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 5 minutes to cook out the raw flour taste. Now add the beef broth and chicken broth. Bring the soup to a boil; reduce the heat to medium low and simmer for 10 minutes. Season to taste with salt and pepper.
When you're ready to eat, preheat the broiler. Arrange the baguette slices on a baking sheet in a single layer. Sprinkle the slices with the cheese and broil until bubbly and golden brown, 3 to 5 minutes.
Ladle the soup in bowls and float several of the cheese croutons on top.
Alternative method: Ladle the soup into bowls, top each with 1 to 2 slices of bread and top with cheese. Put the bowls into the oven to toast the bread and melt the cheese, about 3 to 5 minutes. Yield: 4 to 6 servings.