Soak beans overnight in a large pot and cover with enough cold water so that it comes to about two inches over the top of the beans.
The next day, empty beans into a colander or strainer. Rinse the pot, then set it on medium heat. Heat oil, then add onions, bell peppers, jalapeño, garlic, cumin, chili powder, oregano, crushed chili flakes, and salt. Cook, while stirring occasionally, until vegetables have softened and spices are fragrant. Add beans back into the pot with 6 cups of water or vegetable broth (or a combination of both) and the bay leaves. Reduce heat to low, cover, and simmer for about an hour and a half. If the liquid is too low, add another 1/2 cup.
Taste beans for tenderness and flavoring. Beans should be tender at this point, but continue to cook the soup for another 30 minutes. The liquid will reduce and thicken and beans will continue to break down, creating a thick and velvety soup.
When the soup is just about done, stir in vinegar, lime juice, and zest for brightness and serve over rice with garnishes.
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