1. Preheat the Oven: Preheat your oven to 325°F (165°C) for slow-roasting the short ribs.
2. Cook the Onions: Melt the butter in a large oven-safe Dutch oven over medium-high heat. Add the thinly sliced onions and cook for about 10 minutes, stirring occasionally until they soften and start to caramelize. Season with black pepper.
3. Add Aromatics and Short Ribs: Add the shallots, garlic, thyme, sage, and red chili flakes to the pot. Nestle the short ribs into the mixture, making sure they are partially submerged in the onions.
4. Add Broth and Seasonings: Pour 6 cups of chicken broth over the short ribs, enough to nearly cover the meat. Stir in the tamari or soy sauce. Add the bay leaves and star anise for extra depth. Cover with a lid.
5. Roast the Short Ribs: Transfer the Dutch oven to the preheated oven and roast for 2 1/2 to 3 hours, or until the short ribs are tender and falling off the bone. In the last 1-2 hours of cooking, add the baby carrots.
6. Shred the Meat: Once the short ribs are tender, remove the Dutch oven from the oven. Discard the bay leaves and star anise. Remove the bones and shred the meat using two forks. Return the shredded meat to the soup and keep it warm on low heat. Adjust seasoning with salt if needed.
7. Prepare the Cheesy Gruyère Toast: While the soup simmers, preheat the oven to 425°F (220°C). Arrange the French bread slices on a baking sheet and toast for 10 minutes until crispy.
8. Broil the Cheesy Toast: Switch the oven to broil. Top each slice with a generous amount of Gruyère cheese and broil for 2-3 minutes until bubbly and golden. Keep an eye on them to avoid burning.
9. Serve the Soup: Ladle the rich short rib and onion soup into bowls. Top each with a cheesy Gruyère toast slice. Garnish with fresh thyme and black pepper, and serve immediately. Enjoy the comforting warmth in every bite!