In the bowl of a freestanding electric mixer fitted with a paddle attachment, combine 1 cup dark brown sugar and fresh zest from medium limes. Use your fingers to rub the zest into the sugar until incorporated throughout — this will help release oils from the zest and make your sugar more flavorful.

In a medium bowl, combine 3 1/2 cups all-purpose flour, 2 tablespoons Dutch-processed cocoa powder, 2 teaspoons ground ginger, 1 teaspoon ground cinnamon, 1/2 teaspoon kosher salt, and 1/4 teaspoon ground cloves. Whisk to combine and set aside.

Return to your sugar and zest mixture and add 3/4 cup unsalted butter, 1/2 cup blackstrap molasses, and 2 teaspoons dark rum. Beat on medium speed until smooth; lower the mixer speed to its slowest setting and add 2 egg yolks, one at a time, only adding the next egg yolk when the previous one is fully incorporated. With the mixer still on its slowest setting, add the dry ingredients gradually and continue beating until just combined.

Once the dough has come together, use a rubber spatula to scrape the dough onto a lightly floured surface. Knead gently for 1 to 2 minutes, until the mixture is pretty uniform. Wrap in plastic wrap and transfer to the refrigerator to rest and chill for 1 hour.

When the cookie dough has rested, center a rack in the oven and preheat to 375 (F). Line two baking sheets with parchment paper and set aside.

Transfer the cookie dough from the refrigerator to a lightly floured surface. If the dough is too hard to work with, give it a whack or two with a rolling pin until it becomes more pliable. Use a rolling pin to roll the dough into 1/4-inch thick slab. Use cookie cutters to stamp out cookie shapes. Gather any scraps and reroll, repeating the process until all the dough is used up.

Transfer the cookie shapes onto the prepared baking sheets, leaving 1 inch between each cookie. In theory, the cookies shouldn't spread out that much but will puff up instead. Transfer one baking sheet to the freezer and chill for 10 minutes, before transferring to the preheated oven and baking for 10 minutes. Because the cookies are dark, it can be hard to tell when they're done — they should be firm to the touch but not too firm. Resist the urge to bake them any longer because they'll firm up as they cool! Transfer to a wire rack to cool completely. Repeat with the remaining baking tray.