Add the beans to a pot with enough cold water to cover well. Bring to a boil, lower the heat, cover, and simmer until just soft throughout but not quite cooked, approximately 50 to 80 minutes, depending on the beans. Drain and set aside.
Preheat the oven to 325 degrees F.
Heat olive oil over medium heat in a Dutch oven. Add onion and cook until soft. Add the garlic and cook for 30 seconds. Add tomatoes and their liquid, 2 cups water, honey, cloves, salt, and pepper and boil gently for 20 to 30 minutes or until it begins to thicken. Stir in the parsley and remove from heat.
Place the beans in an oven-proof dish, pour tomato mixture on top, stir and spread mixture out evenly. Bake 1 1/2 to 2 hours, or until beans are soft. (Check the dish during cooking and if needed, add a small amount of boiling water.) The dish will look crispy on top. Remove from the oven and let sit for 10 minutes before serving. Serve hot or at room temperature.