Preheat oven to 375°F. Line two baking sheets with parchment paper and set aside.
In a medium bowl whisk together the flour, baking soda, cinnamon, ginger, cloves, allspice and salt. Set aside.
In a large mixing bowl beat the butter and cream cheese together with an electric mixer until blended. Add 1/3 cup granulated sugar and the dark brown sugar to the butter mixture. Beat on high until light and fluffy. Scrape down the sides and bottom of the bowl with a spatula and beat again until blended.
Add the egg yolk and vanilla and blend on medium speed until incorporated. Add the molasses and mix on low just until blended. Scrape down the sides and bottom of the bowl and mix another 5 or 10 seconds on low.
Add the flour mixture and beat on low speed until almost completely incorporated, about 30 seconds. Scrape down the bowl again and mix the dough one last time using a spatula until no pockets of flour remain. The dough will be soft.
Pour the last ⅓ cup of granulated sugar in a shallow bowl. Scoop out a heaping tablespoon of dough using a small cookie scoop. Lightly form the dough into a 1 ½-inch ball. Roll the dough ball in the granulated sugar until coated. Place on the prepared baking sheet about 2-inches apart. Don't over-fill the pan.
Bake for 8 to 10 minutes or just until the edges are set, the cookies are puffed but still look raw in-between the cracks. The cookies will seem under-baked but this is okay. For a nice chewy cookie, don’t over-bake. Transfer to a wire rack and cool completely before storing.