Melt the stick of butter in a large pot over medium heat. Add the onions, garlic, bay leaf, thyme, and salt and pepper and cook until the onions are very soft and caramelised, about 25 minutes. Add the wine, bring to a boil, reduce the heat and simmer until the wine has evaporated and the onions are dry, about 5 minutes. Discard the bay lead and thyme sprigs. Dust the onions with the flour and give them a stir. Turn the heat down to medium low so the flour doesnâ€™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.
When youâ€™re ready to eat, preheat the broiler. Arrange the baguette slices on a baking sheet in a single layer and brush with the softened butter. Sprinkle the slices with the Gruyere and broil until bubbly and golden brown, 3 to 5 minutes.
Ladle the soup in bowls and float several of the Gruyere croutons on top. Garnish with chives.
Edited: July 31st, 2009