Bonito flakes are made from fillets of a tuna-like fish that are smoked, aged, and shaved into paper-thin slices for a savory, smoky flavor that's impossible to forget. You'll never make this classic without it again.
Melt butter in a Dutch oven over medium-high. Add onions, salt, bay leaves, and thyme sprigs. Cook, stirring occasionally, until onions are soft, about 25 minutes. Reduce heat to medium, and cook, stirring often, until onions are deep golden brown, about 1 hour.
Preheat oven to 375°F. Remove and discard bay leaves and thyme sprigs. Add flour; cook, stirring constantly, 2 minutes. Stir in sherry; cook 1 minute. Stir in beef broth and Quick Bonito Broth; increase heat to high, and bring to a boil. Reduce heat to low, and simmer 15 minutes.
Meanwhile, place baguette slices in a single layer on a rimmed baking sheet. Bake in preheated oven until golden and toasted, about 8 minutes.
Ladle soup into 10 broiler-safe 10- to 12-ounce ramekins or soup bowls. Top each with 3 bread slices, toasted side down. Sprinkle evenly with cheese (about 3 tablespoons per bowl). Working in batches if needed, place bowls on a baking sheet, and broil 2 minutes or until tops are golden and cheese bubbles. Garnish with thyme leaves.
Note: If you do not have oven-safe crocks, flip toasts on baking sheet, sprinkle with cheese, and broil until bubbling and starting to brown. Top soup with cheese toasts.
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