PREHEAT OVEN TO 350F (180C). Set rack at center.
In a large bowl, stir together the dry ingredients: flour, baking soda, cinnamon, cloves, ginger, and salt. Set aside.
In a medium bowl, beat together the wet ingredients: butter, peanut butter, sugar, molasses, fresh ginger, and egg until fluffy on medium speed—2-3 minutes. This will work fine with either a stand mixer fitted with the paddle attachment or with a large bowl and a hand-held electric mixer.
Add the wet ingredients to the dry ingredients and mix well.
Shape into 1-inch balls and roll in sugar or nuts. Place two inches apart on an ungreased cookie sheet and bake, one sheet at a time, about 8 minutes or until cookies are just dry at edges and cracked but still a bit gooey at the center. Turn cookie sheets around once halfway through baking. Do not overbake.
Remove trays to cooling racks and rest for a minute or two. Remove cookies to racks and cool completely. Store in airtight containers for 3-4 days or freeze for up to 3 months.