Heat 2 tablespoons of olive oil in a Dutch oven over medium-high heat. Season the beef short ribs generously with salt and pepper, then add them to the hot oil. Sear for about 3–4 minutes on each side until they achieve a deep, golden-brown crust. Once browned, carefully remove the ribs and set them aside on a plate.

Reduce the heat to medium and add 2 tablespoons of butter to the same pot. When melted, add the thinly sliced yellow onions, stirring them occasionally. Cook for 30–40 minutes until they're deeply caramelized and golden brown. Stir in the minced garlic during the last minute of cooking to enhance the flavor.

Pour in 1 cup of red wine to the caramelized onions, scraping up the delicious brown bits from the bottom of the pot. Allow the wine to simmer for about 2–3 minutes until it reduces slightly.

Return the seared short ribs to the pot along with 6 cups of beef broth, 2 sprigs of thyme, 1 bay leaf, and diced carrots and celery. Increase the heat to bring everything to a gentle boil, then cover and reduce the heat to simmer for 2.5 to 3 hours, or until the meat is fork-tender.

Once the short ribs are tender, carefully remove them from the pot. Shred the meat from the bones, discarding any excess fat, and return the shredded meat along with the caramelized onions back to the broth. Season with salt and pepper to taste.

While the soup simmers, preheat your broiler. Slice a baguette and toast the pieces until lightly golden. Top each slice with grated Gruyère cheese and broil for about 2–3 minutes, or until the cheese is bubbly and golden brown.

Ladle the soup into bowls and place the cheesy toasts directly on top. Garnish with extra thyme and a sprinkle of cracked pepper before serving.