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Step 1
Caramelize the onions. In a large heavy-bottomed stockpot, melt the butter over medium-high heat. Add the onions and sauté until well for about 30 minutes until caramelized (but not burnt), initially stirring every 3-5 minutes, then about once a minute near the end of caramelization to prevent burning*. Add garlic and sauté for 2 minutes. Stir in the flour and cook for an additional 1 minute. Stir in the wine to deglaze the pan, using a wooden spoon to scrape up any browned bits on the bottom of the pan.
Step 2
Simmer the soup. Add the stock, Worcestershire, bay leaf, and thyme and stir to combine. Continue to cook until the soup reaches a simmer. Then reduce heat to medium-low, cover and simmer for at least 10 minutes. Discard the bay leaf and sprigs of thyme. Taste the soup and season with salt and pepper as needed.
Step 3
Toast the bread. Preheat oven to 400°F. While the soup is simmering, slice the baguette into 1-inch thick pieces and arrange them in single layer on baking sheet. Bake for 6-8 minutes, until the bread is toasted and golden around the edges. Remove and set aside.
Step 4
Broil the topping. Switch the oven to the broiler. Once the soup is ready to serve, place your oven-safe bowls on a thick baking sheet. Ladle the soup into each bowl, then top with a baguette slice and your desired amount of cheese (I used about 1/4 cup shredded cheese for each). Place on an oven rack about 6 inches from the heat and broil for 2-4 minutes, or until the cheese is melted and bubbly. (Keep a close eye on them so that they do not burn.) Remove from the oven and serve immediately while the soup is hot and bubbly.