Special equipment: Eight 12-ounce soup crocks
Melt the butter in a very large Dutch oven or pot over medium heat. Add half the onions and sprinkle with 1/2 teaspoon salt and a few grinds of black pepper. Top with the remaining onions and sprinkle with 1/2 teaspoon salt and more pepper. Add the bay leaves and thyme and cook, stirring occasionally, until the onions are very soft and just begin to turn brown, about 1 hour. (The onions will begin to stick to the bottom of the pan and turn brown after about 30 minutes; just keep scraping them up and stirring them into the rest of the onions.)
Add the wine to the pot, bring to a simmer and cook until it has almost completely evaporated, about 4 minutes. Add the beef broth and 1 cup of water, bring to a simmer and cook until the flavors have come together and the soup is rich, about 45 minutes. Season with 1/2 teaspoon salt and a few grinds of black pepper. Either keep the soup warm on a low burner or cool completely, refrigerate and reheat later. (The cooked soup can be refrigerated for up to 2 days or cooled and frozen for up to 1 month.)
Preheat the broiler. Place four soup crocks on a rimmed baking sheet and fill them about 3/4 of the way with hot soup. Float a slice of bread on top of each and cover with Gruyere. Broil until the Gruyere is golden brown (don't be alarmed if some soup bubbles out), 2 to 3 minutes. Repeat with the remaining soup, bread and Gruyere.
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