Cover the pot and transfer it to the preheated oven. Braise the short ribs in the oven for about 2.5 to 3 hours, or until the meat is tender and falling off the bone.
Remove the pot from the oven. Discard the thyme sprigs and bay leaf. Remove the short ribs, shred the meat, and return it to the pot.
Preheat your broiler. Ladle the soup into oven-safe bowls, top each with a slice of baguette, and sprinkle generously with Gruyère cheese.
Place the bowls under the broiler until the cheese is melted and bubbly, about 3-5 minutes. Serve hot.
For a lighter version, you can substitute chicken broth for beef broth and use boneless beef chuck instead of short ribs. If you prefer a vegetarian option, omit the short ribs and use vegetable broth, adding mushrooms for a meaty texture. For a different flavor profile, try adding a splash of balsamic vinegar to the onions during caramelization. You can also experiment with different cheeses, such as Comté or Emmental, for the topping.