Soak the lima beans for at least 8 hours. Drain and rinse the beans, place them in a large pot with cold water and bay leaf. Cover and bring to a boil, then lower the heat to medium heat. Simmer the beans for 30 minutes or until the beans are tender but not fully cooked through. Skim off any foam that collects while cooking.
Drain the beans, reserving 1 cup of the cooking water and the bay leaf, and set aside. Dissolve the bouillon cube in the reserved 1 cup of hot bean liquid, set aside.
Preheat the oven to 375°F. Lightly grease a dutch oven or a baking dish or a casserole pan.
Heat olive oil in a pan or the dutch oven (if using), add the garlic and onion and cook till the onion turns translucent, about 3~4 minutes.
Add the carrot and cook for 1~2 minutes. Next add the tomatoes, reserved bean water, red wine vinegar, tomato paste, maple syrup, oregano, thyme, salt, pepper and nutmeg. Stir and bring the mixture to a boil, then lower the heat and cook for 10~12 minutes, to thicken the sauce.
Check the seasoning and add more salt and pepper, if needed. Add the beans, parsley and mint.
Transfer the beans to the baking dish (if using the dutch oven, just transfer it to the oven), cover the pan with foil, and bake the beans, stirring occasionally, for 30~40 minutes, or until the beans are tender and the interior of the beans is creamy.
Remove the foil and bake for another 10~15 minutes, to thicken the sauce a little and the beans are slightly dry.
Remove from the oven, remove the bay leaf, and allow to cool for 10 minutes before serving.