In a medium bowl, whisk together the 3 cups all-purpose flour, baking soda, salt, ground ginger, ground cinnamon, ground cloves, and ground nutmeg until evenly combined.
In a large bowl, beat the softened unsalted butter and dark brown sugar with a hand mixer (or stand mixer) on medium speed until light and fluffy, 2–3 minutes, scraping the bowl as needed.
Add the unsulphured molasses, large egg, and vanilla extract to the butter mixture and beat until smooth, about 1 minute.
Add the dry ingredients in two additions, mixing on low just until a soft dough forms and no dry patches remain. If the dough seems very sticky, let it rest 5 minutes to allow the flour to hydrate.
Divide the dough in half, flatten each portion into a 1-inch-thick disk, wrap tightly, and chill until firm, at least 2 hours and up to 24 hours.
When ready to bake, preheat the oven to 350°F. Line two baking sheets with parchment paper.
Dust the work surface with the 0.25 cup all-purpose flour for dusting. Working with one disk at a time, roll the dough to 1/4 inch thick, lightly dusting the top and pin as needed to prevent sticking. Cut out shapes and transfer to the prepared sheets, spacing about 1 inch apart. Gather and re-roll scraps once.
Bake, one sheet at a time, until the edges are set and the centers look slightly soft, 8–10 minutes for chewy cookies or 10–12 minutes for crisper cookies; rotate the sheet halfway through baking for even browning.
Let cookies cool on the sheet for 5 minutes, then transfer to a wire rack to cool completely before serving or decorating.