Heat a 12 to 14-inch saucepan over medium heat. When the pan is hot, add the duck pieces, skin side down. The duck skin will provide more than enough fat for browning without adding excess oil. Cook, occasionally pouring excess fat off carefully, until golden brown, about 8 minutes per side.
Meanwhile, in medium-sized saute pan, heat the olive oil over medium heat until hot but not smoking. Add the onion, celery, and carrot, and saute over medium heat until softened, about 12 minutes. Add the fennel seeds, pine nuts, cloves, raisins, bay leaves, flour and 1/2 cup vinegar and continue cooking for 2 minutes. Add duck pieces and 1/4 cup vinegar. Season with salt and pepper. Bring to a boil, cover and lower the heat. Braise over low heat until the sauce is thick, about 30 to 40 minutes. Remove the cloves.
Remove the duck to a large plate and spoon vegetables over.
Stir the chocolate and sugar into the cooking liquid. Serve sauce with the duck and garnish with chopped parsley, red pepper flakes and a drizzle of extra-virgin olive oil.