Go through the beans and remove any foreign materials. Then rinse them in a colander.
Pour beans into a large pot and cover with 3 or 4 inches of water. Soak beans overnight covered or for around 12 hours. Or use the quick soak method listed above. Drain all the water and rinse.
In a pot or dutch oven that you are going to cook the beans in, sauté onion for 5 minutes or so until translucent, set aside.
Cover beans with about 3 to 4 inches of fresh water in a large pot or dutch oven.
Bring to a boil for 5 minutes then lower the heat to low and cook for 2 hours. If water evaporates, add in more water or vegetable broth to keep beans covered with 2 inches of liquid.
Preheat the oven to 350 degrees. Drain the beans, keeping one cup of cooking liquid.
Combine the beans with the sautéed onion, tomato paste, cider vinegar, maple syrup, dry mustard, salt, and pepper in a baking dish or a dutch oven.
Bake covered for 1 hour.