Combine crust ingredients; press into the bottom and 1-1/2 in. up sides of a 9-in. springform pan. Refrigerate.
For topping, combine the sugar, flour, cinnamon and nutmeg in a Dutch oven; stir in lemon juice. Add apples. Bring to a boil; cover and simmer for 15 minutes or just until apples are tender, stirring. Remove from the heat; stir in pecans. Cool to room temperature. Set aside 3 tablespoons for filling; refrigerate remaining topping until serving.
Combine the cream cheese, eggs, sugar and vanilla in a large bowl; mix until well blended. Add reserved topping; mix well. Pour into crust.
Bake at 350° for 50 minutes. Turn oven off, but leave cheesecake in oven with door ajar for 1 hour. Cool to room temperature. Refrigerate for at least 4 hours. Just before serving, top with apple topping. Yield: 12 servings.