Preheat the oven to 350°F (175°C). Set out oven-safe soup bowls on a rimmed baking sheet.

Heat olive oil and butter in a Dutch oven over medium heat. Add sliced onions with a pinch of salt and cook, stirring occasionally, until deeply golden and jammy, 25–30 minutes. If browning too fast, lower the heat and splash in a tablespoon of water to deglaze.

Push onions to the sides (or transfer to a plate). Increase heat to medium-high. Season short ribs with salt and pepper, then sear in batches until well browned on all sides, about 2–3 minutes per side.

Return onions to the center (if removed). Add thyme and bay leaves. Pour in beef broth, scraping the pot bottom to release browned bits. Bring to a gentle simmer, then reduce heat to maintain a light simmer.

Cover partially and simmer until ribs are very tender, about 2 hours, stirring occasionally. Taste broth; add a small splash of apple cider vinegar if it needs brightness. Season with salt and pepper as needed.

Transfer ribs to a board. Remove bones and excess fat; shred or slice meat. Skim any surface fat from soup, return shredded beef to the pot, and discard bay leaves.

Ladle hot soup into oven-safe bowls. Top each with a toasted sourdough slice and a generous mound of shredded Gruyère.

Bake 10–15 minutes until cheese is melted, then broil 1–3 minutes if needed to brown the top. Serve carefully (hot bowls) with freshly cracked pepper.