Preheat oven to 350-degrees. Line a 13x9 pan with aluminum foil and apply nonstick spray or butter.
In a medium bowl, combine the flours, cinnamon, ginger, allspice, cloves, baking soda, and salt. Stir in most of the chocolate chips; coating them with flour will keep them from sinking as they bake. Set bowl aside.
In a big mixing bowl, combine the butter and two sugars until light and fluffy, scraping down the sides of the bowl as needed. Add the egg, vanilla extract, and pumpkin puree. Once that's mixed, slowly blend in the dry ingredients until just combined.
Pour the batter into the ready pan and smooth out. Sprinkle the remaining chocolate chips over the top.
Bake for 30 to 35 minutes, until it passes the toothpick test in the middle. Cool completely. Lift up by the foil and place on a cutting board to cut bars. Store in a sealed container at room temperature or chilled.
OM NOM NOM!