Generously season the short ribs with salt and black pepper.

In a large Dutch oven, heat the olive oil over medium-high heat. Brown the short ribs on all sides, then remove them and set aside.

Add butter and a splash of olive oil to the pot. Toss in the sliced onions and cook on low heat for 30 to 40 minutes, stirring occasionally, until they are caramelized and golden.

Stir in the minced garlic and cook for a minute. Pour in the dry red wine to deglaze the pot, scraping up any bits stuck to the bottom. Allow it to reduce for a few minutes.

Pour in the beef stock, add fresh thyme and bay leaves, then return the browned short ribs to the pot. Cover and simmer over low heat for 2.5 to 3 hours until the meat is fall-apart tender.

While the soup is simmering, toast the baguette slices under the broiler until golden. Top each slice with shredded Gruyère cheese and return to the broiler until melted and bubbly.

Remove the bay leaves and thyme stems from the soup, ladle it into bowls and top with the Gruyère toast. Serve hot.