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Place beans in a large bowl and add 1 gallon water. Stir in two tablespoons kosher salt. Set aside at room temperature and let rest overnight. The next day, drain and rinse beans. Transfer to a large Dutch oven. Add bay leaf, split onion, and 3 quarts water. Bring to a boil over high heat, reduce to a bare simmer, cover, and cook until beans are completely tender and skins are loose, 2 to 2 1/2 hours. Discard onion and bay leaves. Drain beans, reserving liquid. (See note for pressure cooker or canned bean variations).
Heat vegetable oil in a large Dutch oven over medium-high heat until shimmering. Add onions, garlic, and jalapeño (if using) and cook, stirring frequently, until softened but not browned, about 3 minutes. Add beans and chipotle (if using) and cook, folding with a wooden spoon until homogenous. Add 2 cups of reserved bean liquid. Mash beans with a potato masher until desired consistency is reached, adding extra cooking liquid as necessary to loosen to desired texture. If smoother texture is required, use a hand blender or a food processor to process beans to desired texture. Season with salt to taste. Serve. Uneaten beans can be stored in an airtight container in the refrigerator for up to 5 days.