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 ribs on all sides until a deep brown crust forms, about 3-4 minutes per side. Remove and set aside.

Reduce heat to medium-low, add butter to the pot. Once melted, add the sliced onions and cook slowly for 45-60 minutes, stirring occasionally, until they are deep brown and caramelized. Add the minced garlic and cook for another minute until fragrant.

Pour in the red wine to deglaze the pan, scraping up any browned bits. Allow the wine to reduce by half. Return the seared short ribs to the pot along with any juices.

Add the beef broth, fresh thyme sprigs, and bay leaves. Bring to a simmer, then reduce heat to low, cover, and cook for 2.5-3 hours, or until the beef is fall-apart tender.

Remove the bones, thyme stems, and bay leaves. Shred the beef in the pot with two forks. Taste the soup and adjust seasoning with salt and pepper.

Preheat your broiler. Ladle the soup into oven-safe crocks. Top each with a slice of toasted baguette and a generous amount of shredded Gruyere cheese. Place on a baking sheet and broil for 2-3 minutes, watching closely, until the cheese is melted, bubbling, and has blistered brown spots.

Carefully remove the crocks from the oven. Garnish with fresh thyme leaves and serve immediately.