Combine the flour, salt, and pepper. Dredge the lamb in the flour mixture. Heat the olive oil in a Dutch oven, then add the lamb. Sear on all sides until golden, 3 to 4 minutes per side. Remove the lamb and set aside.
Add the shallots, garlic, cloves, and allspice and cook until the mixture is a rich brown, about 5 minutes. Add the stock, wine, and tomatoes. Using a wooden spoon, scrape any brown bits from the bottom of the pot. Return the lamb to the pot, cover tightly, and transfer to oven. Cook until the lamb is fork-tender, 2 1/2 to 3 hours.
Place the lamb on serving dishes and put the pot over moderately high heat. Add the olives, orange zest, and orange juice and bring to a simmer. Reduce the liquid until slightly thickened, 3 to 5 minutes. Ladle it over the lamb and sprinkle on the chives.