Preparation
Preheat the oven to 325 degrees F. Arrange the short ribs on a large sheet of foil. Sprinkle all over with 1 teaspoon salt and 1 teaspoon pepper. Bring New Mexico chilies, ancho chilies, and 1 1/2 cups water to a simmer in a medium saucepan over high heat. Cover; reduce heat to medium-low and simmer until chilies are just tender, 5 to 6 minutes. Transfer the mixture to a blender. Holding the top on firmly, blend until chili puree is smooth.

Heat oil in a large pot over medium-high heat. Add the short ribs in batches and brown on all sides, about 5 to 6 minutes per batch, transferring short ribs to a bowl each time. Add chopped red onion and garlic to drippings in pot. Sauté until onions soften, about 5 minutes. Mix in cumin and oregano. Add chili puree from blender, broth, agave, and espresso; stir to blend. Return short ribs and any juices from bowl to pot; stir to coat. Bring to simmer. Cover and place pot in the oven. Braise until the ribs are very tender, about 2 hours 30 minutes.

Tilt pot. Spoon off and discard any fat that rises to surface and pools at lower end. Using tongs, transfer ribs and any loose bones to a rimmed baking sheet. Carefully cut membrane off each piece of meat (try to cut away only the membrane not any meat). Discard membranes and all bones. Cut meat into small (scant 1/2 inch) cubes. Return meat to sauce in pot. Mix in black beans. Season chili with about 1/4 teaspoon each of additional salt and pepper. If desired, add adobo sauce by teaspoonfuls to increase the spiciness. Transfer chili to a large bowl. Sprinkle with green onions.
Spoon polenta into deep bowls. Ladle chili over. Sprinkle generously with chocolate. Serve with garnishes.
Cook Time: about 2 hours 45 minutes
Inactive Prep Time: 20 minutes
Prep Time: about 45 minutes