Put beans into a large bowl, cover with 12 cups cold water, and set aside in a cool place to soak overnight. Crush 6 of the garlic cloves and 1 tsp. salt together with a mortar and pestle to a smooth paste. Stir in 1 tsp. of the cumin, then the olive oil and lime juice. Transfer to a large glass or ceramic bowl, add quail, and turn in marinade until well coated. Cover and refrigerate overnight.
The next day, put beans and the soaking water (you should have about 10 cups) into a large wide heavy-bottomed pot with a tight-fitting lid. Add 1 of the onions and 4 of the culantro leaves, cover, and bring to a boil over medium-high heat. Reduce heat to medium-low and simmer until beans are soft, 1–1 1⁄2 hours. Remove and discard onion. Transfer 1 cup of the cooked beans to a medium bowl, mash with a fork to a smooth paste, then stir paste back into pot of beans. Remove pot from heat.
Preheat oven to 350º. Scrape marinade off quail and set marinade and quail aside separately. Chop the remaining 4 cloves garlic, the remaining onion, and the remaining 4 culantro leaves and set each aside separately.
Heat annatto oil in a large skillet over medium-high heat. Working in batches, add quail and brown on each side, 2–3 minutes per side, then transfer to a plate; set aside. Reduce heat to medium, add chopped garlic, and cook, stirring, until soft, about 30 seconds. Add chopped onions and chives and cook, stirring often, until onions are translucent, about 5 minutes. Add tomatoes, cilantro, oregano, chopped culantro, and the remaining 1 tsp. cumin, season to taste with salt and pepper and cook, stirring often, until mixture cooks down to a paste . 7-10 minutes.
Add to the tomato mixture, quail, and the reserved quail marinade to beans in pot and stir to combine. Cover and bake until quail is cooked through and liquid thickens, about 1 hour. Adjust seasonings.