In a large heavy-bottom pot, melt the butter over low heat. Add the sliced onions, thyme, salt, and pepper and continue to cook, stirring occasionally until the onions become a deep golden brown and very soft, about 30 minutes.
Add the flour and cook for 1 to 2 minutes. Add the white wine and scrape up any dry bits on the bottom of the pan, increasing the heat to a boil for 2 to 3 minutes. Add the beef stock, and the chicken stock, and allow the soup to simmer for an additional 30 minutes as the flavors develop. Season the soup generously with salt, and pepper, to taste.
Preheat the oven to broil, or turn on the broiler. Arrange the ciabatta cubes on a baking sheet and toast until crispy, about 3 to 5 minutes.
Remove the thyme sprigs and pour the soup into 4 to 6 oven-safe crocks or bowls. Top with the toasted ciabatta cubes and a generous amount of grated Gruyere.
Place the crocks or bowls under the broiler for 3 to 5 minutes, or until the cheese is melted and begins to brown.