Whisk the all-purpose flour, baking soda, ground cinnamon, ground ginger, ground cloves, and sea salt together in a medium bowl until well combined.
In a large mixing bowl, beat the softened salted butter and packed brown sugar with an electric mixer until the mixture is light and fluffy.
Add the molasses, room-temperature egg, and vanilla extract to the butter mixture and continue beating until the texture is smooth.
Turn the mixer to low and slowly add the dry flour mixture, mixing just until the white streaks disappear.
Cover the dough tightly and place it in the refrigerator to chill for at least one hour to prevent spreading.
Preheat the oven to 350°F and line two large baking sheets with parchment paper.
Roll the chilled dough into balls about 1.5 to 2 tablespoons in size and place them two inches apart on the prepared sheets.
Bake in the center of the oven until the edges are set and the tops are slightly puffed, usually taking between 9 and 11 minutes.
Allow the cookies to rest on the hot baking sheet for five minutes before moving them to a wire rack to cool completely.