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Preheat oven to 450°F. Toss squash and onion in large bowl.
Mix butter, brown sugar, vanilla, salt, nutmeg and pepper in small bowl until well blended. Pour over squash mixture; toss to coat well. Arrange in single layer on foil-lined large shallow baking pan.
Bake 15 minutes. Add apples; toss to mix well. Bake 25 to 30 minutes longer or until squash and apples are tender.