How to Make It
Heat a large skillet. Add the ancho, pasilla and guajillo chiles and toast over moderately low heat, turning, until lightly charred, about 4 minutes. Transfer the chiles to a heatproof bowl. Cover with the boiling water and let stand until softened, about 20 minutes.
Drain the chiles and transfer to a blender. Add the chipotles and coffee and puree until smooth. Add the ale; pulse until blended.
Heat the oil in a large, enameled cast-iron casserole. Season the short ribs with salt and pepper and add half to the pot. Cook over moderately high heat until browned all over, about 8 minutes. Using a slotted spoon, transfer the meat to a plate. Lower the heat to moderate and brown the remaining short ribs. Return all of the meat to the casserole and cook until heated through, about 1 minute.
Add the onion and garlic to the casserole and cook over moderately high heat until softened, about 3 minutes. Add the coriander, cumin, cinnamon and cloves and cook until fragrant. Add the chile-ale mixture and the chicken stock and bring to a simmer, stirring. Cover partially and simmer over low heat until the meat is very tender and the sauce is slightly reduced, about 2 hours.
Ladle 2 cups of the sauce into a heatproof bowl and whisk in the masa harina. Whisk the mixture into the pot and simmer until the sauce thickens, 15 minutes. Stir in the chocolate. Season the chili with salt and hot sauce; serve with cheddar, onion and tortillas.
Masa harina, a type of corn flour, is available at Latin American markets and many supermarkets and health-food stores.