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1
Sort through the beans and discard any stones. Put beans in a medium bowl and cover with cold water to cover by at least two inches. Cover with plastic wrap and soak overnight.
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2
Drain beans, rinse, and place in a large pot along with the onion, garlic, bay leaf, thyme, and salt, and add enough fresh water to cover the beans by one inch. Bring to a boil, reduce heat to low and simmer until a bean mashes easily between your fingers, about 1 hour. Turn off the heat and let the beans cool a bit and absorb more of the cooking liquid.
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3
Preheat the oven to 300 degrees. In a large dutch oven over medium heat add the olive oil and diced pancetta. Cook until the pancetta is crisp and brown, then remove with a slotted spoon. Add the peeled cipolline to the pan and saute, stirring occassionally, until the onions are well browned on all sides, about 12-15 minutes. Add the beans, pancetta, and sage to the cipolline and pour in enough of the bean cooking liquid to come just below the top of the beans (about 2 cups). Bring to a simmer and then transfer to the oven.
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4
Bake, uncovered for 2 hours. Check the pot periodically to make sure the mixture is bubbling softly, and add more liquid if the level falls more than 1/2 an inch below the surface of the beans.
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5
Remove from the oven and stir in the chopped parsley and balsamic vinegar. Drizzle with olive oil and sprinkle with sea salt. Serve with good crusty bread.