Preheat oven to 375 degrees F. Line two baking sheets with parchment paper.
In a medium bowl, whisk together the flour, baking soda, cinnamon, ginger, cloves, allspice, pepper and salt; set aside.
Using an electric mixer, beat together the butter and both sugars on medium-high speed until light and fluffy, about 3 minutes. Reduce the speed to medium-low, add the egg yolk and vanilla extract, increase the speed to medium and beat until thoroughly combined, about 30 seconds. Again reduce the speed to medium-low and add the molasses, beating until fully incorporated, about 30 seconds, scraping the sides of the bowl halfway through. Reduce the speed to low and gradually add the dry ingredients, mixing until just incorporated, about 30 seconds. Use a rubber spatula to give it a final few mixes to ensure no flour remains.
Place the sugar for rolling in a small bowl. Using a tablespoon or small cookie scoop, scoop the dough and roll into a smooth ball, then toss in the sugar to coat and place on the prepared baking sheet. Repeat with the remaining dough. Bake the cookies, one sheet at a time, until the cookies are browned, still puffy and the edges have begun to set but the centers are still soft, about 11 minutes. Be sure not to overbake the cookies.
Allow the cookies to cool on the baking sheet for 5 minutes, then remove to a wire rack to cool completely. The cookies can be stored in an airtight container at room temperature for up to 5 days.