Combine the whole-wheat flour, all-purpose flour and salt in a large bowl or a food processor. Work in 12 tablespoons cold butter using a pastry blender or 2 knives or by pulsing in the food processor until it is pebble-sized. Add ice water, 1 tablespoon at a time, stirring with a fork or pulsing, until the dough is evenly moistened (but not wet) and is just starting to clump together. Be careful not to overmix.

Divide the dough into 2 equal pieces. Pat each one into a 5-inch disk. Wrap in plastic wrap and refrigerate for at least 1 hour or for up to 2 days.

Remove the dough from the refrigerator and let stand until softened slightly, about 15 minutes.

Combine the brown sugar, softened butter, ground cinnamon, vanilla and salt in a small bowl.

Set aside until needed, at room temperature so that it will spread easily.

Stir together the apples, flour, sugar, lemon juice, cinnamon, vanilla and salt in a large bowl until the apples are evenly coated. Set aside until needed.

Roll one piece of dough between 2 sheets of parchment or wax paper into a 13-inch circle. Peel off the top sheet and invert the dough onto a 9-inch deep-dish pie pan. Place in the refrigerator, covered, while working on the dough for the top crust.

Roll the second piece of dough between 2 sheets of parchment into a 12-by-16-inch rectangle. Evenly spread the cinnamon topping over the dough. Starting at the long side, tightly roll the dough into a log. Using a serrated knife, cut the dough log into 1/4-inch-thick slices, rotating with each slice to keep slices round. Transfer the slices to a parchment-lined baking sheet and freeze for about 15 minutes or refrigerate for about 30 minutes, or until firm.

Position a rack in the lower third of the oven. Preheat to 425°F.

Remove the pie pan with the bottom crust from the refrigerator. Peel off the parchment. Pour the apple filling into the crust. Gently maneuver the slices within the crust to be sure they all lie as flat as possible.

Once you’re satisfied with the placement of the apple slices, arrange the cinnamon swirl slices over the apple mixture to cover evenly. The top will not be entirely covered; you'll have small spaces here and there. Fold the edges of the bottom crust under and crimp.

Bake the pie for 25 minutes at 425°F. Reduce the oven temperature to 375°F and continue baking until the topping is golden brown and the filling is bubbling, 30 to 40 minutes more.

Let cool on a wire rack for at least 1 hour before serving. If desired, sprinkle lightly with powdered sugar.