Preheat oven to 300 degrees.
Bake tortillas directly on the oven shelf for 15-20 minutes, turning once until crisp right through. They will break with a clean snap. Break into coarse pieces and set aside.
Spread onion pieces out in a heavy frying pan. Cook over moderate heat without stirring until the onions are sizzling and begin to stick to the pan. Stir in the stock and let it bubble up, stirring up the browned deposits in the pan as it bubbles. Stir in the garlic and the spices. Turn the heat down and simmer, stirring frequently until the mixture is thick, not at all soupy, and the onions and spices are frying in their own juices. Don't rush this step. It is essential that the spices should not have a harsh raw taste.
Stir in the black beans and heat gently. Mash roughly while still in the pan, with a potato masher. You want a rough lumpy mixture, not a smooth puree. Set aside.
In a gratin dish, spread a layer of a third of the tortilla pieces. Spread a layer of the black beans over the tortillas and spread 1/3 of the tomato sauce over the black beans. Sprinkle with 1/3 of the cheese. Repeat this, ending with a layer or the beans, sauce and cheeses.
Bake for 30 minutes covered. Uncover, and bake for 5-10 minutes more. Serve garnished with lime wedges.