Start by seasoning your beef short ribs generously with salt and black pepper. In a large Dutch oven, heat a drizzle of olive oil over medium-high heat. Sear the short ribs for about 10 minutes, turning occasionally, until they develop a rich, brown crust on all sides. Remove the ribs from the pot and set them aside, allowing the juices to settle.

In the same pot, add a mix of butter and a splash of olive oil. Lower the heat to medium and toss in thinly sliced yellow onions. Cook them for about 30-40 minutes, stirring occasionally, until they turn beautifully golden brown and caramelized.

Once your onions are perfectly caramelized, stir in minced garlic and cook for an additional minute. Then, deglaze the pot with a cup of dry red wine, scraping up any browned bits from the bottom. Allow the mixture to simmer for a few minutes until the wine reduces slightly.

Return the browned short ribs to the pot, along with fresh thyme and beef stock. Bring the soup to a gentle boil, then cover and reduce the heat to low. Allow it to simmer for 2.5 to 3 hours, or until the meat is tender.

While the soup is simmering, preheat your broiler. Slice a French baguette into thick pieces, and toast them until they are crisp. Layer generous amounts of Gruyère cheese on each slice and place them under the broiler for 2-3 minutes until the cheese is bubbly and golden.

Before serving, remove bay leaves from the soup. Ladle the soup into bowls, and top each serving with a slice of cheesy baguette. Serve hot.