Mix tapioca with sugars, salt, cinnamon, and 1/2 teaspoon nutmeg.
Fold in apple slices.
Pour mixture into a deep 8-inch square baking dish.
Roll pastry into an 8-inch square.
Cut several slits near center of pastry and arrange pastry on apples.
Bake in preheated hot oven (425 °F.) for about 35 minutes.
Serve with whipped cream spiced with nutmeg.