In a large bowl, combine all of the apple filling ingredients: apples, flour, ¼ cup brown sugar, granulated sugar, vanilla, cinnamon, nutmeg and salt. Stir and then set aside. It's ok if everything is not well combined at this point, because the apples will release some of their juices while you prepare the topping and then you will stir the apple mixture again.
6 cups (2.75 pounds) peeled Granny Smith apples, sliced or chopped (no more than ¼-inch thick)*, ¼ cup all-purpose flour, ¼ cup packed brown sugar, 2 tablespoons granulated sugar, 1 teaspoon vanilla extract, 1 teaspoon ground cinnamon, ¼ teaspoon ground nutmeg, ¼ teaspoon salt