Drain the beans, cover with fresh water by a couple of inches, and bring to a boil with the bay leaf. Lower the heat and let the beans simmer while you prepare the rest of the ingredients.Heat a small heavy skillet over medium heat. Add the cumin seeds, and when they begin to color, add the oregano, shaking the pan frequently so the herbs don't burn. When the fragrance is strong and robust, remove the pan from the heat and add the paprika and cayenne. Stir spices and remove from the pan. (The paprika and cayenne only need a few seconds to toast.) Grind in a mortar or coffee mill to a coarse powder.
Heat the oil and sauté the onions over medium heat until they soften. Add the garlic, salt, ground herbs, and chili powder, and cook another 5 minutes. Add the tomatoes, their juice, and about a teaspoon of the chilpotle chili. Simmer for 15 minutes; then add this mixture to the beans, along with enough water (if necessary) so the beans are covered by at least 1 inch. Continue cooking the beans until they are soft, an hour or longer, adding water if necessary.
When the beans are cooked, taste them, and add more chilpotle if desired. Season with the vinegar, more salt if needed, and chopped cilantro. Serve with garnishes.
Chilpotle chilies are a smoked pepper, sold in cans in Mexican groceries. They are worth the search -- they add a wonderful smoky hotness to the dish. (But if you can't find them, go ahead and make it anyway!) Freeze the rest of the can for next time - or smear a little inside a grilled cheese sandwich or quesadilla.