2. In an ovenproof dish, place the butternut squash cut side down. In a small bowl, combine the shallots, oil and season with salt and pepper, mixing well. Place the shallots around the squash and bake until very tender and slightly caramelized, about 45 minutes to 1 hour. Remove from the oven and allow to cool. Cut the shallots into large dice. Spoon the squash from the skin and cut into large dice. Reserve.
3. In a large saucepan, combine the cranberries, water and sugar. Bring to a boil over high heat, then turn down to simmer cooking until the cranberries are tender, about 30 minutes. Transfer to a colander, drain the cranberries and reserve the cooking liquid. Add enough additional cranberry juice to the cooking liquid to measure 4 cups and return to the saucepan.
4. Bring the cranberry liquids to a simmer over medium high heat. Add the couscous and cover with a tight fitting lid. Stir occasionally, cooking until tender, about 20 minutes. Remove from the heat and transfer to a large oven proof casserole. Add the cooked cranberries, roasted shallots, squash, chives and rosemary. Season with salt and pepper. Cover with a lid or foil and keep warm in the oven until serving.