1. Thinly slice the onions. In a large pot, melt the butter over low heat. Add the onions and cook slowly, stirring occasionally, until they are deeply caramelized, about 5 hours.
2. Increase the heat to medium and pour in the port wine and sherry. Allow the mixture to simmer until the alcohol reduces by half.
3. Add the beef stock and thyme bundle to the pot. Reduce the heat to low and let simmer for another hour, allowing the flavors to blend.
4. While the soup is simmering, prepare the croutons. Cut the crusty bread into slices, lay them on a baking sheet, and toast in the oven until golden brown.
5. Once the soup is ready, ladle it into bowls, top each with a slice of toasted bread, and generously sprinkle with Emmental or Gruyere cheese.
6. Place the bowls under the broiler until the cheese is perfectly melted and bubbly.
7. Serve immediately, enjoying the combination of hearty soup and creamy cheese.