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Soak the beans overnight in cold water. Although I am not normally a huge fan of soaking (especially because I use super fresh beans from places like Rancho Gordo), I think it is important in this dish as you will not be just straight cooking the beans like normal.
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The next day, place the beans in a large pot with their water--add enough additional water to cover by 2 inches. Bring to a boil, skimming the foam, and add one bay leaf. Cover and let very gently simmer until the beans are tender but not mushy. For me this was about 1 hour, but I like to let the beans barely simmer.
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In the meantime, place the meat in a large pot and cover with cold water. Add the other bay leaf and bring to a boil. Skim the foam and reduce the heat to a bare simmer. Let cook for about 60 minutes at a very slow simmer (if you simmer it harder, remove at about 30 minutes). I like lower and slower.
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While the beans and meat are cooking, bring a small pot of lightly salted water to a boil. Blanch the orange zest strips 3 times (Wolfert does not address why you do this, but it definitely made the zest tender and easy to chew). When you are done, use a knife or scissors to shred the zest into skinny strips. Set aside.
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Remove the meat, reserving the cooking broth, and set aside to cool. Boil the remained broth down to 1 cup.
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Drain the beans, reserving about 1 cup of the bean broth. Set both aside.
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Cut the pork into 1/2-inch pieces--it should be juicy and barely cooked. Sprinkle with salt and pepper.
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While the pork broth is reducing, heat a large, straight-sided skillet over medium high heat. Add the extra virgin olive oil. When it is hot, add the onion with a pinch of salt and cook for 5 minutes. Add the pork and garlic and cook for another 3 minutes, then add the beans. Cook for 1 minute. Stir in the Aleppo, crushed mustard seeds, wine, reduced pork broth, orange juice and zest, chopped tomatoes and scant teaspoon of salt. Bring to a boil, reduce the heat to maintain a gentle simmer, and cover. Let simmer for 30 minutes. If it seems to have too little liquid, add some reserved bean broth.
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Preheat the oven to 400 F. Taste the beans for additional seasoning, but note that the broth will be decidedly orange and decidedly alcoholic at this point (I was really nervous!); both of the these attributes will mellow after baking.
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Place the pork and beans into a baking dish (2 1/2 qt). Bake for 45 minutes, during which time a lot of the liquid will cook off (if it cooks off before the 45 minute mark, take it out then). My liquid never completely cooked off, so I served it with rice (couscous would work too) and it was fantastic so I did not worry about it.
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Serve warm with rice or couscous--or without, to your taste. Place additional Aleppo flakes at the table for those who would like it spicier.