Don't have time to soak the beans overnight?
Put them in a 4-quart saucepan. Add enough cold water to cover by 2 inches and bring just to a boil. Remove from the heat and soak for 2 hours. Drain the beans and continue with the recipe.
Sort through the beans to make sure there are no little stones and then put them in a large bowl or pot. Add enough cold water to cover the beans by 2 inches and let soak overnight. Drain the beans well, tilting the colander instead of shaking it to gently extract the water and protect the beans’ skins.
Position a rack in the center of the oven and heat the oven to 300°F.
Cook the bacon in a 5- to 6-quart Dutch oven over medium-high heat, stirring occasionally, until golden brown, about 8 minutes. Remove the pot from the heat and with a slotted spoon transfer the bacon to a small bowl. Pour off and discard all but 3 Tbs. of the fat.
Set the pot over medium heat and add the onion and garlic. Cook, stirring occasionally, until soft and golden, about 7 minutes. Add the broth, mustard, nutmeg, cloves, and 1 tsp. pepper. Stir to combine. Add the beans and bring just to a simmer over medium-high heat. Cover and bake until the beans are easy to bite into but still a little mealy in texture, 45 to 60 minutes.
Stir in the reserved bacon and the apple, cider, maple syrup, ketchup, and marjoram, and bake, uncovered, until the beans are fully tender, 30 to 60 minutes more. Cool to room temperature, remove the marjoram stems, cover, and refrigerate overnight.
To finish, bring to a simmer, uncovered, over medium heat. Reduce the heat to low and continue to simmer until the sauce is reduced to the consistency of thin gravy, stirring occasionally so the bottom doesn’t burn, 40 to 60 minutes. Stir in the vinegar (if using) and season the beans to taste with salt and pepper.
These slightly sweet and savory beans are great with sausages or roast pork.