Preheat oven at 350 and oill mini cupcake can.
In a large bowl mix together flours, sugar, ginger, cinnamon, salt and baking soda, then set aside.
In another bowl mix together the applesauce, molasses, egg, and oil. Add the wet ingredients into the dry ingredients and mix until well combined. (Batter will be wet)
Using a mini cooke scooper, place the dough into the mini cupcake pan. Bake for 10-12 minutes or until golden brown.
Remove from oven and using a cap from a water bottle press into the cookie to make a crater. Allow to cool completely.
To make the filling, in a small bowl beat the whip cream until it forms a stiff peak, set aside. Then in another small bowl beat the cream cheese and vanilla extract, then add the confectioners sugar and mix until well combined. Gently fold in the whip cream, then place the filling into the cookie cups.
Serve chilled.