Place rack in center of your oven and preheat oven to 350 degrees F. Line an 8-inch x 8-inch baking dish with parchment paper and spray lightly with nonstick cooking spray.
In a large bowl, combine the whole wheat flour, 1 cup all purpose flour, oats, brown sugar, baking soda, cinnamon, salt, all-spice, and nutmeg. Add the butter in small pieces, then quickly work it in with your fingers, until the mixture resembles coarse crumbs. Set aside.
In a small bowl, whisk together the caramel and remaining 3 tablespoons of flour. Set aside.
Press 2/3 of the crumbs into the prepared baking dish and evenly arrange the sliced apples over top. Then evenly pour the caramel over the top of the apples and sprinkle with the remaining crumbs.
Bake for 30 to 40 minutes, or until top is lightly browned. Let the bars cool completely before cutting—or serve very messy, very delicious bars immediately.
TO STORE: Leftover caramel apple bars may be kept in the refrigerator for up to 5 days in an airtight container.
TO FREEZE: Caramel apple bars may be stored in the freezer for up to 3 months. Thaw overnight in the refrigerator before serving.
TO REHEAT: Enjoy these bars chilled from the fridge, at room temperature, or warm. To reheat, warm an individual serving on a microwave-safe plate for 10-20 seconds.