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Reduce the heat to medium-low and add the carrots, celery, onions, and leeks and season lightly with salt and pepper. Cook, stirring occasionally, until vegetables are golden and very tender, 45 minutes to 1 hour - you may need to add a bit of water towards the end of the cooking time if the vegetables begin to stick to the pan. (It is important to cook the vegetable mixture for this length of time to get a rich, deep basis for the ragout.) Add the wine and duck livers and cook, stirring, until mostly evaporated, about 1 minute. Add the tomatoes, bay leaves, garlic cloves, oregano, red pepper, and herb sprigs and cook, stirring, until mixture is almost dry, about 15 minutes. Return all of the duck and bacon to the pan along with 3 cups of the stock and bring to a boil. Reduce the heat to a simmer and partially cover the Dutch oven. Cook, stirring occasionally, until the duck is tender, up to 6 hours, depending on the type of duck you use. You will need to add more stock little by little as the sauce reduces; you may not need all 6 cups. (Or, if you run out of stock and the duck is still not tender, add a bit of water as necessary.) The sauce should be thick but not so thick that it browns on the pan bottom. Season with salt and pepper, to taste. Remove the duck pieces from the sauce and set aside to cool. Remove the bay leaves and herb sprigs and discard.
When the duck meat is cool enough to handle, remove the skin and discard. Shred the meat into bite size pieces and return it to the Dutch oven. Cook until the sauce is very thick and flavorful and the meat is very tender, 20 to 30 minutes longer. Add the chicken livers, parsley, and thyme; stir to combine and cook for 5 minutes longer. Taste and re-season if necessary. Remove from the heat.