Preheat the oven to 325° F.

In a large oven-safe Dutch Oven over high heat, melt together the butter and onions. Cook 5 minutes, until softened. Add the wine, season with pepper, and continue cooking another 5-8 minutes, until the wine has evaporated and the onions are lightly golden. Add the shallots, garlic, thyme, sage, and chili flakes. Then add the short ribs. Pour over 6 cups of broth. Add the tamari, bay leaf, and star anise (if using). Cover and roast in the oven for 2 ½ to 3 hours or until the short ribs are tender and falling off the bone. Add the carrots during the last 1-2 hours of cooking.

Remove the bay leaves and star anise. Discard any bones and extra fatty pieces. Lightly shred the meat. Taste and season with salt, if needed. Place over LOW heat on the stove.

Switch the oven to 425°. Arrange the bread on a baking sheet and toast for 10 minutes, until very dry. Switch the oven to broil. Top the toast with cheese, then broil until bubbly, 2 to 3 minutes.

Ladle the soup into bowls. Top with cheesy toast, black pepper, and fresh thyme. Eat!