How to Make It
Drain and rinse the beans. In a large saucepan, cover the beans with 6 cups of the water and bring to a boil. Reduce the heat to low, cover and simmer until tender, about 1 hour. Meanwhile, soak the chipotle in the 1/2 cup of boiling water until softened, about 20 minutes. Drain the chipotle. Discard the stem and seeds and mince the chile.
Heat the olive oil in a large saucepan. Add the onion and cook over moderate heat until softened, 2 to 3 minutes. Add the bacon and cook until softened, 2 to 3 minutes longer. Stir in the remaining 4 cups of water and the chipotle, brown sugar, tomato paste, wine, nutmeg, cloves, cumin, paprika and chili powder. Drain the beans and add them to the saucepan. Cover and simmer over low heat until the sauce has thickened, about 1 hour. Stir in the chocolate, season with salt and pepper and serve.