Pat the short ribs dry and season generously with salt and pepper. Heat olive oil in a large Dutch oven over medium-high heat. Sear the short ribs on all sides until deeply browned, about 3-4 minutes per side. Remove from the pot and set aside.

Reduce heat to medium. Add butter to the pot. Once melted, add the sliced onions and a pinch of salt. Cook, stirring occasionally, for 30-40 minutes until they are soft, jammy, and deeply caramelized.

Stir in the minced garlic and cook for 1 minute until fragrant. Pour in the red wine to deglaze, scraping up any browned bits from the bottom of the pot. Bring to a simmer and let it reduce by half.

Return the seared short ribs to the pot. Add the beef broth, thyme sprigs, and bay leaf. Bring to a simmer, then reduce heat to low, cover, and cook for 2.5-3 hours, or until the beef is tender.

Carefully remove the short ribs from the soup. When cool enough to handle, remove the meat from the bones, shred it, and discard any large pieces of fat. Return the shredded beef to the soup. Remove and discard thyme sprigs and the bay leaf. Season the soup with salt and pepper to taste.

Preheat the broiler. Ladle the soup into oven-safe bowls. Top each with 1-2 baguette slices and a generous amount of shredded Gruyère cheese. Place on a baking sheet and broil for 2-3 minutes until the cheese is melted and bubbly. Serve immediately.