Ingredients:

1 cup dry starchy beans, rinsed (Pinto are a good choice.)
1/3 cup diced onion
1 tablespoon maple syrup
1 tablespoon tomato paste
1 teaspoon molasses
1 teaspoon mustard
1 teaspoon tamari
1 teaspoon apple cider vinegar

Spices (your preference):
1/8 teaspoon ground cloves
1/2 teaspoon ground garlic
1/2 teaspoon ground onion
1/2 teaspoon paprika (or smoked paprika, ancho, chipotle, cayenne)
1/8 teaspoon black pepper
1/8 teaspoon turmeric
1/4 to 1/2 teaspoon salt

2 teaspoons fine ground corn meal or corn flour mixed with 2 teaspoons cold water (optional)

Directions:

1. Bring beans and about 2 quarts of water to a boil in a heavy pot or dutch oven, on stovetop. Lower heat and simmer for 2 hours or until beans are soft. (Adding salt to the boiling water will keep the beans more intact but I don’t do this because I like them a bit mushy.) Add water to keep level about an inch above beans. Do not drain beans.
2. Preheat oven to 320 degrees.
3. Stir together maple syrup, tomato paste, molasses, mustard, tamari, vinegar, and corn meal liquid if using. Add to beans along with onions. Add spices.
4. Cover pot and bake for 2 to 3 hours (depends on how mushy you like your beans). Check often to stir and add water if getting too dry.

This recipe requires about 4 or 5 hours cooking time, compared to 8-12 hours or overnight, which is more traditional.* You can cut the time by precooking the beans on the stovetop before adding maple syrup, tomatoes, vinegar and other ingredients that slow bean softening. Daniel Gritzer explains this and much more in his post:
How to Make Boston Baked Beans, the Low, Slow, Old-Fashioned Way, Serious Eats, 2016

You can also cook everything on the stovetop and not use the oven. Just add the onion after about 2 or 3 hours, let that cook with the beans for 30 minutes, then add the ingredients in number 3 above. Continue simmering for about 20-30 minutes depending on how thin or thick you want the final product. I’ve done both oven and stovetop and can comfortably say that all-stovetop is not inferior.

*The Bean Hole:

A tradition in Maine, of “bean hole” cooking, may have originated with the native Penobscot people and was later practiced in logging camps. A fire would be made in a stone-lined pit and allowed to burn down to hot coals, and then a pot with 11 pounds of seasoned beans would be placed in the ashes, covered over with dirt, and left to cook overnight or longer. These beans were a staple of Maine’s logging camps, served at every meal.

“Removing the cover of the bean hole at an early convention [Springfield Telescope Makers, Vermont], likely in the 1930’s.” Source: Stellafane.org