Cream together the butter and sugars in the bowl of a stand mixer with a paddle attachment until light and fluffy. Add the egg, applesauce, and vanilla and beat until well combined. Scrape the bowl as needed.
Add in the baking powder, soda, salt, cinnamon, and nutmeg. Mix until well incorporated. Add the flours and mix until barely combined. Mix in the oats, carrots, cranberries, and chocolate chips until just mixed.
Stir with a rubber spatula to make sure everything is well incorporated. Cover the bowl with plastic wrap and refrigerate for at least one hour or overnight.
Preheat the oven to 350 ˚F and line your cookie sheets with parchment paper.
Use a two-tablespoon scoop to portion the dough on the cookie sheet about 2 inches apart. Bake for 15 minutes or until just set.
Move to a wire rack to cool completely.