In a large Dutch oven, melt the butter over medium heat.

Once bubbling, add the onions and a generous pinch of salt. Cook, stirring occasionally, until the onions become translucent, about 10 minutes. Add another pinch of salt and the sugar. Continue to cook, stirring occasionally, until onions are deeply golden brown and caramelized, about 45 minutes. Be sure to add small splashes (1 tablespoon at a time) of water if the onions ever become too dark or dry.

Once onions are caramelized, add the flour and cook, stirring frequently until the flour turns golden and forms a paste, 2 to 3 minutes. Add the wine to deglaze and bring to a simmer, making sure to scrape up any browned bits from the bottom of the pot. Simmer until slightly thickened, about 2 minutes.

Stir in the beef stock, thyme sprigs, dried bay leaves, and pepper to taste. Bring to a simmer and cook, stirring occasionally, until flavors meld, 20 minutes. Taste and adjust for seasoning and remove from the heat. Use tongs to remove the dried bay leaves and thyme stems.

Meanwhile, preheat the oven to 375°F. Arrange the baguette slices onto a sheet pan and brush the tops with olive oil. Bake until golden and crisp, 8 to 10 minutes. Remove from the oven and set aside.

Preheat the broiler and ladle the soup into ramekins or small bowls. Sprinkle about 1 ¼ cups of the Gruyère evenly among the bowls. Top each with two to three pieces of toasted baguette onto each. Finish by evenly dividing the remaining 1 ¼ cups of Gruyère overtop.

Transfer to the oven and broil until the cheese is melted, bubbling, and golden brown, 2 to 3 minutes.

Garnish with fresh thyme leaves and serve immediately.