In a large heavy-bottomed skillet or Dutch oven, heat the butter and olive oil over medium heat until butter foams. Add the thinly sliced onions, sugar, and 1/2 teaspoon of the salt. Cook, stirring every 2–3 minutes, until onions soften and begin to turn golden (about 15 minutes). Reduce heat to medium-low and continue to cook, stirring more frequently, until deeply golden-brown and caramelized, 25–35 minutes more. If onions begin to stick, reduce heat and stir; add a tablespoon of water if needed to deglaze and prevent burning.

Deglaze and build flavor

Increase heat to medium-high, add the Cabernet, and scrape any browned bits from the pan with a wooden spoon. Allow the wine to reduce by about half, 2–3 minutes. Stir in the flour and cook 1–2 minutes to remove raw flour taste.

Simmer the soup

Slowly whisk or stir in the beef stock until smooth. Add the remaining 1/2 teaspoon salt, the black pepper, bay leaf, thyme sprigs, and Worcestershire sauce. Bring to a gentle simmer, reduce heat to low, and simmer, partially covered, for 20 minutes to let flavors meld. Taste and adjust seasoning; remove and discard the bay leaf and thyme sprigs before serving.

Croutons and Cheese Topping

Prepare ciabatta croutons

Preheat oven to 375°F (190°C). Brush both sides of the ciabatta slices lightly with olive oil. Place on a baking sheet and toast until lightly golden and crisp, 8–10 minutes, flipping once. Remove from oven and rub one side of each toasted slice with the halved garlic clove while still warm to impart a hint of garlic.

Assemble cheeses

Combine grated Swiss and shredded mozzarella in a small bowl. Reserve about 1 tablespoon of Parmesan if using for finishing.

To Finish and Bake in Cups

Preheat the broiler (or set oven to 450°F/230°C if you don't have a broiler). Arrange 4 ovenproof soup crocks or cups on a baking sheet.

Ladle the hot onion soup into each crock, filling to about 3/4 full to leave room for the crouton and cheese.

Place one ciabatta crouton on top of each filled crock. Sprinkle an even portion of the Swiss/mozzarella mixture over the crouton so cheese covers bread and spills slightly onto soup surface. Finish each with a light dusting of the reserved Parmesan, if using.

Place the baking sheet with crocks under the broiler about 4–6 inches from the heat source. Broil until cheese is melted, bubbly, and golden-brown in spots, 2–4 minutes (watch carefully to avoid burning). If using a high-temp oven instead, bake at 450°F (230°C) for 6–10 minutes until cheese is melted and browned.

Carefully remove crocks from oven using oven mitts. Let cool 2 minutes, garnish with fresh thyme leaves and a crack of coarse black pepper, and serve hot. Warn diners that cups will be very hot.