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Soak the beans in water: Pre-soak the beans, either by covering with two inches of water and soaking overnight, or by pouring boiling water over them and soaking them for an hour.
Drain beans, cover with water, cook until tender: Drain the beans and put them in a medium-sized pot and cover with 2 inches of water. Bring to a simmer, cover, reduce the heat to a low simmer and cook until the beans are just soft enough to eat, about 1 hour, give or take 15 minutes or so, depending on how old the beans are (older beans will take longer to cook).
Cook bacon or pancetta: Preheat the oven to 325°F. In a 3 or 4 quart heavy-bottomed, oven-proof, lidded pot such as a Dutch oven, heat the olive oil over medium heat. Add the bacon or pancetta and cook slowly until lightly browned and crispy.
Sauté onions: Add the chopped onions and increase the heat to medium-high. Cook, stirring often, until the onions begin to brown. Use a wooden spoon to scrape any browned bits off the bottom of the pot.
Add garlic, chili flakes, sage, then add tomatoes and stock: Add the garlic, chile flakes and sage and cook for 1-2 minutes, then add the honey and tomato paste. Stir well to combine.Add the tomatoes or tomato sauce and the stock. Bring to a simmer. Taste for salt and add some if needed.
Add the beans, cover, cook in oven: Drain the beans and add them to the pot. Stir well.Cover the pot and cook in a 325°F oven for 1 hour and 15 minutes.If still a bit wet, remove the cover and cook for 15 minutes more. Note that the cooking time will depend on several things, the most important being how thoroughly the beans were cooked to begin with when they were simmered.If the beans are still a bit hard when they go in the oven, it may take several hours to soften them, once the tomato and honey have been added.
Stir in parsley and balsamic vinegar: Right before serving, gently stir in the chopped parsley and balsamic vinegar. Taste for salt, add more if needed to taste.Serve either hot or at room temperature.