Sift the flour, cocoa powder, ground ginger, cinnamon, cloves and nutmeg into a medium bowl; set aside.
Put butter and grated ginger into the bowl of an electric mixer fitted with the paddle attachment. Mix on medium speed until lightened, about 4 minutes. Add brown sugar; mix until combined. Add molasses; mix until combined.
Mix in the flour mixture in 2 batches, alternating with the baking soda mixture. Mix in chocolate. Transfer dough to a piece of plastic wrap. Pat dough to about 1-inch thick; wrap in plastic. Refrigerate until firm, about 2 hours (or overnight).
Preheat the oven to 325°F. Line 2 baking sheets with parchment paper. Roll dough into 1½ inch balls and space 2 inches apart on baking sheets. Refrigerate 20 minutes.
Roll balls in granulated sugar. Bake until surfaces crack slightly, 10 to 12 minutes. Let cool on sheets 5 minutes. Transfer to wire rack, and let cool completely.
Notes
Cookies are best the day they are made, but can be stored in airtight containers at room temperature up to 5 days. You can also freeze these. Just store in a tightly covered container and defrost when ready for munching.