Whisk together the all-purpose flour, ground ginger, ground cinnamon, ground nutmeg, ground cloves, baking soda, and salt in a medium bowl.

Cream the softened unsalted butter, brown sugar, and granulated sugar together in a large mixing bowl until light and fluffy, about 2-3 minutes.

Add the egg yolk and vanilla extract to the creamed mixture and mix until well combined.

Gradually add the dry ingredients to the wet mixture and stir gently until just combined. Fold in the finely chopped pecans.

Chill the dough for 30 minutes in the refrigerator.

Preheat the oven to 350°F. Line a baking sheet with parchment paper. Scoop tablespoon-sized portions of the dough, roll them into balls, and place them on the baking sheet, spacing them about 2 inches apart. Create an indentation in the center of each cookie.

Bake for 10-12 minutes or until the edges are lightly golden. Let them cool for 5 minutes before transferring to a wire rack.