Dry the beef well, then season all sides with the salt and black pepper. Dry meat takes on color quickly, while damp meat tends to turn pale and release moisture.
Heat 1 tbsp olive oil over high heat in a heavy-based pot, then brown the beef pieces on every side for 3 to 5 minutes total before transferring them to a plate. A deep mahogany crust and browned bits on the pot signal that the flavor foundation is ready.
Lower the heat to medium-low and add the remaining 2 tbsp olive oil, garlic, and onion; cook for 2 minutes, then add the carrots and celery and cook slowly for 5 minutes. The vegetables should smell sweet and aromatic and soften without developing dark color.
Add the crushed tomatoes, tomato paste, crumbled bouillon cubes, wine or broth, water, thyme, and bay leaves, then return the beef and any collected juices to the pot. Bring the liquid up to a simmer before lowering the heat until the surface barely moves.
Cover the pot and cook on low for 2 to 2 1/2 hours, checking the beef at the 2-hour mark. The meat is ready when a fork can pull apart the fibers with little resistance; well-marbled pieces may soften sooner.
Lift out the beef, shred it coarsely with two forks, and stir it back into the sauce before simmering uncovered on low for 30 minutes. The sauce should reduce to a thick consistency that lightly coats the back of a spoon.
Taste the ragu and adjust with salt and pepper, adding 1/2 tsp sugar if the tomatoes taste too sharp, then cover the pot until serving. The finished sauce should taste balanced, deeply savory, and rich without a harsh acidic edge.