Preheat oven to 350 degrees.
Cream together butter and sugar until smooth. Add in egg and yolk and mix until blended. Add molasses, ginger, cinnamon and cloves and mix well.
In a separate bowl, combine flour, baking soda and salt. Stir gently. Slowly add to mixer, letting each addition mix in before adding more.
Roll 1/2 Tbsp of dough and place into the wells of a mini muffin pan. Gently press with your thumb to create an impression.
Bake for 10 minutes at 350 degrees. Remove from the oven and, with a small spoon, scoop out the middle of the cookie to create a cup. Cool completely and then remove from pan.
Meanwhile, beat together cream cheese and butter until smooth. In 1/4 cup amounts, add in powdered sugar letting each addition fully mix in before adding more.
With the mixer running, add milk until frosting is desired consistency. Pipe into the center of cooled cookie cups. Sprinkle with nutmeg.