Preheat oven to 350° F. Line a cupcake pan with 12 liners
In a large bowl, whisk together flours, sugar, baking powder, baking soda, cinnamon, nutmeg and salt until blended
Add egg, applesauce and oil. Mix with an electric mixer on medium low for 2 to 3 minutes, stopping once or twice to scrape the sides of the bowl.
Stir in chopped apple.
Fill the cupcake liners ½ - ¾ full. Bake 18-20 minutes. Remove from oven and cool completely on a cooling rack.
While the cupcakes are baking, in a small bowl mash together the cream cheese and brown sugar. Add the maple syrup a tablespoon or so at a time to thin the icing. This is not buttercream frosting it will not be thick and fluffy. It is meant to be a slightly runny glaze.
If it seems like it is getting too runny, don't add the full amount of syrup. Put in fridge until cupcakes are baked and cool. It will thicken upon standing.
Remove icing from fridge and stir. Add more maple syrup to thin if necessary. Using a teaspoon, scoop out a small amount of cake from the top of the cupcake, then fill the hole and the top of the cupcake with a tablespoon or so of icing. Add the removed scoop of cake on top for decoration.
Alternate: do not scoop out a bit of cake and add an apple slice on top. This should be done immediately before serving to prevent the apple from become brown and unappealing.