Preheat oven to 350º. Season chicken with salt and pepper. In large oven-proof saute pan, heat oil over medium high heat. Add chicken thighs, skin side down, and sauté until well browned, about 4 minutes. Turn and sauté another 4-5 minutes. Remove from pan and reserve.
To same pan, add onion, cumin, paprika, nutmeg, cinnamon, allspice, and cayenne. Saute, stirring, until onion is softened and beginning to brown, about 2-3 minutes. Add red wine vinegar and stir, scraping up any brown bits in the pan. Bring to a boil and cook for another minute.
Add tomatoes to pan and top with chicken. Place pan, uncovered, in oven and roast for 35-40 minutes or until chicken is tender and registers 170º on an instant read thermometer.
While chicken is roasting, make Lima Bean Puree.
In a small saucepan, combine beans, 2 cups water, and garlic. Bring to a boil and cook until beans are very tender, about 20 minutes. Drain, reserving liquid.
Add almonds to processor; pulse until well blended. Add beans and process until combined. With machine running, gradually add oil, scraping down sides as needed. Add lemon juice, salt, and pepper. If puree is too thick, add cooking liquid to loosen, one tablespoon at a time. The puree should be the consistency of slightly loose mashed potatoes.
To serve, spoon puree on individual plates or a platter. Place chicken thighs on puree (or next to) and spoon tomato sauce over chicken.