In a large bowl, cream together the shortening, brown sugar, molasses, egg, and vanilla. In a separate bowl, whisk together the flours, baking powder, baking soda, cinnamon, ginger, cloves, and salt. Gradually stir the dry ingredients into the wet. Cover the bowl and refrigerate the dough until chilled (I stick it in the freezer for 10 to 15 minutes).
Preheat oven to 375F and line 2 large baking sheets with parchment paper or silpat liners. Scoop the dough out with a 1 ½ tablespoon measure and roll it into balls. Arrange on the prepared baking sheets about 3 inches apart (they will spread out quite a bit as they cook; I do 6 cookies per half sheet pan).
Put a little bit of sugar in a shallow bowl. Grease the bottom of a glass with butter and dip it in the sugar. Flatten each ball of dough slightly, re-greasing and sugaring as necessary.
Bake until they’re set along the edges, about 10 to 12 minutes, rotating the trays once halfway through (be sure not to over-bake!). Cool for a couple minutes on the tray, then transfer to a wire rack to finish cooking. Bake the remaining dough the same way.