Heat the oven to 350°F (175°C). Cover a large baking sheet with parchment paper or a silicone baking mat to keep the cookies from adhering during baking. Set the prepared pan aside.
In a large mixing bowl, thoroughly whisk together the 3 cups all-purpose flour, 2 teaspoons baking soda, 2 teaspoons ground ginger, 1 teaspoon ground cinnamon, 1/4 teaspoon ground cloves, 1/4 teaspoon allspice, and 1/2 teaspoon salt. Continue whisking until the spices and leavening are evenly dispersed throughout the flour, then reserve the mixture.
Place the softened unsalted butter, 2/3 cup granulated sugar, and 2/3 cup packed brown sugar in the bowl of a stand mixer fitted with the paddle attachment. Beat at medium-high speed, approximately settings 6–8, for 5–8 minutes. Stop several times to scrape the bottom and sides of the bowl. The finished mixture should appear noticeably lighter and fluffy.
Add the room-temperature egg, 1/3 cup molasses, and 2 teaspoons vanilla extract to the creamed butter mixture. Begin mixing at low speed, then gradually raise the mixer to medium speed. Beat until the ingredients are completely blended, scraping the bowl whenever necessary for uniform incorporation.
Add the reserved flour mixture to the wet ingredients in two additions. Mix initially at low speed, then increase to medium-high as needed, periodically scraping the bowl. Continue only until no visible streaks of dry flour remain.
Cover the mixing bowl securely with plastic wrap and refrigerate the dough for at least 1 hour or as long as overnight. When the dough has been refrigerated overnight, leave it at room temperature for approximately 15 minutes before portioning so that it softens slightly.
In a small bowl, combine the 1/2 cup granulated sugar, 1 teaspoon cinnamon, and 1/2 teaspoon ground ginger, whisking until the spices are evenly distributed.
Using a 1.5-tablespoon cookie scoop, portion the chilled dough and roll each portion between your palms to create a smooth ball. Coat every dough ball completely in the spiced sugar mixture.
Arrange the coated portions on the prepared baking sheet, allowing at least 1 inch of space between the cookies.
Bake the cookies for 9–12 minutes, stopping when the edges appear set and cracks begin to form across the tops.
Leave the freshly baked cookies on the baking sheet for approximately 10 minutes. Transfer them afterward to a wire cooling rack and allow them to cool completely. Their texture will become firmer as they cool.