Sear Beef: Season the short ribs with salt and pepper. Heat olive oil in a Dutch oven over medium-high heat. Sear the ribs until browned on all sides. Remove and set aside.
Sauté Sofrito: Lower heat to medium. Add onion, carrot, celery, and garlic, cooking for 3-5 minutes. Deglaze with red wine, cooking an additional 3 minutes.
Build the Ragu: Add beef broth, bouillon paste, crushed tomatoes, tomato paste, cheese rind, salt, pepper, oregano, basil, bay leaves, crushed red pepper, and thyme. Return short ribs to the pot.
Simmer: Bring to a boil, then reduce heat and cover. Simmer for 2 hours.
Shred Meat: Remove the bay leaves, thyme, and cheese rind. Shred the meat from the ribs, discarding the bones.
Finish the Ragu: Return the shredded meat to the pot. Simmer for an additional 30 minutes. If thicker sauce is desired, mix some sauce with cornstarch and return to pot.
Cook Pasta: Boil pasta in salted water until al dente. Transfer using tongs directly to the ragu sauce and toss.
Serve: Serve the ragu over pasta, garnished with fresh parmesan or burrata, flaked sea salt, and chopped basil.