Season short ribs with salt and pepper. Heat olive oil in a large Dutch oven over medium-high heat and sear short ribs on all sides until browned. Remove and set aside.

In the same pot, sauté chopped onions, carrots, and celery for 4–5 minutes until softened. Add garlic and tomato paste and cook 1–2 minutes.

Deglaze the pot with red wine, scraping up browned bits. Let reduce 2–3 minutes.

Return short ribs to the pot. Add beef broth, thyme sprigs, and bay leaf. Bring to a simmer, cover, and cook on low heat for 2–2.5 hours until meat is tender.

While ribs cook, melt butter and olive oil in a separate pan over medium-low heat. Add sliced onions and sugar. Cook slowly 25–30 minutes until deep golden brown. Deglaze with brandy or sherry if using.

Remove short ribs from broth, shred meat, and discard bones. Strain broth to remove vegetables if desired. Return shredded meat and caramelized onions to broth.

Preheat oven broiler. Place bread slices on a baking sheet and top with shredded Gruyère. Broil 2–3 minutes until cheese melts and is bubbly.

Ladle soup into bowls and place Gruyère toast on top. Garnish with fresh thyme if desired and serve immediately.