In a medium bowl, whisk the flour, ginger, cinnamon, baking soda, salt, nutmeg, and pepper.
In a large bowl, beat the butter and brown sugar with a stand mixer fitted with the paddle attachment on medium speed until light and fluffy, about 3 min. Add the egg yolk and molasses and mix until well blended, about 1 minute. Add the flour mixture and mix on medium-low speed until the dough is well blended and forms moist pebbles, 30 to 60 seconds.
Dump the dough onto an unfloured work surface; gently knead until it comes together. Shape into an 8-inch-long log about 1-1/2 inches in diameter and wrap in plastic. Refrigerate until firm, about 3 hours.
Position a rack in the center of the oven and heat the oven to 350°F. Line two large cookie sheets with parchment or nonstick baking liners.
Unwrap the dough and use a thin, sharp knife to cut the log into 3/16-inch slices. Arrange the slices about 1 inch apart on the sheets. Bake one sheet at a time until the cookies are slightly darker brown on the bottoms and around the edges, 10 to 12 min. Set the sheet on a rack to cool for 15 minutes. Transfer the cookies to a rack and let cool completely. When cool, store in airtight containers.
Ginger flavor intensifies with time, making these cookies excellent candidates for long keeping. When stored in an airtight container, the cookies remain impressively delicious for up to five days from baking. Well wrapped, the cookies will keep for several weeks in the freezer.