In a heavy 5-quart pot melt the butter over low heat. Add the onions, butter, thyme, bay leaf, garam masala and salt to taste and cook until the onions are deep amber and exceedingly soft, stirring occasionally, 25 to 30 minutes. Add the beef broth and let the soup simmer for 25 to 30 minutes, allowing the flavors to meld together. Season with salt and pepper to taste.
Preheat the oven to broil. Arrange a rack in the middle of the oven. Place the protein bread on the middle rack of the oven and toast until crispy, about 2 to 3 minutes per side.
Remove the bay leaf and thyme sprigs from the soup and discard. Pour the soup into two ovenproof bowls, float the toasted protein bread on top, and cover it with a thick layer of the Gruyère. Put the soup bowls under the broiler on the middle rack and cook 3 to 5 minutes, or until the cheese is fully melted and golden. Best served fresh.