Step 1Cut the meat into 2- or 3-inch pieces and place in a non-reactive bowl.
Step 2Cut one of the onions in half and stick 2 cloves in each half. Cut one of the remaining onions in half lengthwise, then thinly slice crosswise. Peel and slice half the carrots. Add to the bowl with the meat, along with 1 bouquet garni, 1 strip of orange peel, the nutmeg, juniper berries, wine, and vinegar, and toss together. Cover tightly. Refrigerate for 8 to 24 hours, stirring the mixture two or three times.
Step 3Slice the remaining onion and carrots. Place a colander over a large bowl and drain the meat and vegetables into the colander. Remove the pieces of meat, blot thoroughly dry with paper towels, and set aside. Discard the bouquet garni and the orange peel.
Step 4In a large, heavy skillet, heat one tablespoon of the olive oil. Add the meat to the pan in batches and brown slowly on all sides, adding more olive oil if necessary, taking 8 to 10 minutes for each batch. Do not crowd the pan. Transfer to a large, heavy casserole and immediately sprinkle over 1 teaspoon salt and several grinds of pepper, or to taste. Pour off the fat from the pan.
Step 5Return the pan to medium heat, and add 2 tablespoons olive oil and the sliced onion that was not included in the marinade. Cook, stirring and scraping the bottom of the pan to deglaze, until the onion softens, about 5 minutes, then add the sliced onion and carrots from the marinade. Reduce the heat to medium-low and cook the onions and carrots together slowly, stirring often, until lightly colored, about 10 minutes. Add the garlic and stir until fragrant, 30 seconds to 1 minute, then add the flour and cook, stirring for a few minutes. Transfer the mixture to the casserole.
Step 6Remove the skillet from the burner and place the casserole with the meat and vegetables over medium heat. Add the marinade, tomato paste, and the remaining bouquet garni and orange peel. Bring slowly to a gentle simmer, skimming off any foam. Add salt to taste (at least 1 teaspoon), reduce the heat to very low, cover and simmer for 3 hours, stirring occasionally. Add the remaining carrots, cover and simmer until the meat is fork-tender, another 30 minutes to an hour. Taste and season with salt and pepper. Refrigerate overnight.
Step 7Skim any visible fat off the top of the daube. Bring slowly to a simmer. Simmer for 30 minutes to an hour. Taste, adjust seasonings, and serve with pasta, rice, polenta or potatoes.