Preheat the oven to 325°F.

Rinse the short ribs under cool water, and pat them dry with paper toweling. Sprinkle the salt, pepper, and ½ teaspoon of the dried thyme all over the ribs. Heat the oil or lard in a large, heavy-bottomed skillet until hot, then add the ribs in batches without crowding, and cook, turning as needed, until they are deeply browned on all sides. Transfer the browned short ribs to a baking dish or casserole just large enough to hold them, and set aside.

Carefully pour off all but 2 tablespoons of the cooking fat from the skillet, and immediately add the onions to the pan. Sprinkle 1 teaspoon salt over the onions, and stir well. Cook the onions over medium heat, and, using a wooden spoon, scrape the bottom of the skillet as they cook to dislodge any caramelized bits left from browning the ribs. Add the bay leaves, a few grindings of black pepper, and the remaining ½ teaspoon dried thyme. Stir well to distribute the seasonings. Add the whole garlic cloves and cook 3 minutes longer. Pour in the tomatoes, stock, and red wine, bring to a simmer, and cook for 5 minutes. Taste carefully for seasoning. The braising vegetables and liquid should be highly seasoned.

Pour the vegetables and liquid over the browned ribs, and spread the vegetables around so they are in an even layer. Cover with a piece of parchment paper and a double thickness of heavy-duty aluminum foil, shiny side down. Seal tightly, and put in the center of the preheated oven to cook for 1½ hours, or until a paring knife pierces the meat easily. Uncover, and bake 30 minutes longer, basting often, to caramelize the ribs. Remove from the oven and spoon off any visible fat. Taste the braising juices carefully for seasoning, and correct if necessary. Serve hot, with the vegetables and braising juices spooned over as a sauce.