Place an oven rack in the center position and preheat the oven to 375 degrees F. Line two baking sheets with parchment paper.
In a medium-sized bowl, whisk the flour, baking soda, cinnamon, ginger, cloves, allspice, pepper, and salt until evenly combined.
In a stand mixer fitted with the paddle attachment, cream the butter, brown sugar, and 1/3 cup granulated sugar on medium-high speed until pale and fluffy, around 3 minutes. Reduce the speed to medium-low, then add the yolk and vanilla. Increase speed to medium and mix for 20-30 seconds until evenly combined. Scrape down the bottom and sides of the bowl with a rubber spatula. Reduce the speed to medium-low and add the molasses, mixing until fully incorporated, about 20 seconds. Again, scrape the bowl with a spatula.
Turn the speed down to the lowest setting, then add the flour mixture and beat until just incorporated, around 30 seconds, scraping the sides and bottom of the bowl once. Give the dough a final stir to ensure that no pockets of flour remain at the bottom.
Place the remaining 1/2 cup granulated sugar in bowl or shallow dish. Using a tablespoon-sized measuring scoop (or a measuring spoon), portion the dough and use your hands to roll into balls. Drop the dough balls into the sugar bowl, swirling to coat evenly. Place the cookie dough onto the prepared baking sheets spaced about 2 inches apart.
Bake one sheet at a time until cookies are browned, puffy, cracking, and the edges have begun to set but the centers are still soft, around 11 minutes, rotating the baking sheet after 5 minutes. The cookies might look raw between the cracks when they’re ready. Do not overbake! Don’t bake both sheets at once or chill the dough first; you’ll get less of those signature cracks.
Cool cookies for 5 minutes, then use a spatula to transfer them to a cooling rack; cool cookies to room temperature, then serve. Molasses cookies can be stored at room temperature in airtight container or zipper-lock plastic bag for up to 5 days.
If you have some, try using 1/2 cup demerara sugar in place of granulated white sugar for tossing the cookies after rolling. I wouldn't purchase it just for these cookies, but demerara sugar has a lovely, subtle caramel flavor that works well here.Barely adapted from Cook’s Illustrated