Mix the dry ingredients. In a medium-sized mixing bowl whisk the flour, ginger, cinnamon, cloves, baking soda, and salt together until well mixed.
Combine the wet ingredients. Mix the melted butter, dark brown sugar, molasses, egg yolk, and warm water in a separate mixing bowl until fully combined.
Combine the two mixtures. Start by pouring half of the dry ingredient mixture into the bowl with the wet ingredients and mix them well. Then, incorporate the remaining dry ingredients and thoroughly blend the mixture. The result will be a sticky and thick dough.
Chill the dough. Cover the dough with plastic wrap and place it in the fridge to chill for 3 hours and up to 3 days. Chilling is necessary.
Prep. Take the cookie dough out of the refrigerator and let it sit at room temperature for 10 minutes. If chilled for over 3 hours, extend the wait to about 20 minutes for easier scooping and rolling. Preheat oven to 350°F (177°C). Line large baking sheets with parchment paper or silicone baking mats.
Scoop the dough and roll in sugar. Scoop and roll balls of dough, about 1.5 Tablespoons of dough each, into balls. Roll the balls in the granulated sugar first and then into the powdered sugar making sure to coat them.
Bake. Bake the cookies for 11-12 minutes until the edges set, but the centers remain soft. Tip: If the cookies aren't spreading by the 9-minute mark, remove them, tap the baking sheet on the counter 2-3 times to promote spreading, and then continue baking in the oven.
Cool. Allow the cookies to cool for 5 minutes on the baking sheet before transferring them to a wire rack to finish cooling.