Whisk the dry ingredients: In a large bowl, combine flour, baking powder, baking soda, cinnamon, ginger, cloves, nutmeg, and salt. Set aside.
Cream the butter and sugar: In another large bowl, beat softened butter and brown sugar together until light and fluffy, about 2–3 minutes.
Add the wet ingredients: Mix in molasses, egg, egg yolk, and vanilla extract until smooth.
Combine the dough: Gradually add the dry mixture into the wet mixture, stirring until just combined. Dough will be thick and slightly sticky.
Chill the dough: Divide into two discs, wrap tightly in plastic wrap, and refrigerate for at least 2 hours or overnight.
Preheat oven: Heat oven to 350°F (175°C) and line baking sheets with parchment paper.
Roll and cut: On a lightly floured surface, roll dough to ¼ inch thick. Cut into shapes with cookie cutters.
Bake: Place cookies 1 inch apart on prepared sheets. Bake 8–10 minutes, until edges are set but centers are slightly soft.
Cool and decorate: Let cookies cool on the pan for 5 minutes before moving to a wire rack. Decorate once fully cooled.