Preheat oven to 350 degrees. Line two baking sheets with parchment paper.
In a large bowl, whisk together flour, salt, baking powder, baking soda, cinnamon, ginger, cloves and nutmeg. Set aside.
With an electric mixer, beat the sugars and oil together until combined. Stir in the pumpkin puree, eggs and vanilla and mix until combined. Stir in the flour mixture until completely combined.
Use an ice cream scoop with a release mechanism to drop the batter onto the prepared baking sheets, about one inch apart. Bake for 12-15 minutes, or until cookies start to crack and a toothpick inserted in the center comes out clean. Cool cookies completely on the baking sheets.
Meanwhile, make the cream cheese filling by beating all the ingredients with an electric mixer until smooth and creamy.
Spoon or pipe the filling onto half of the pumpkin cookies. Place a second cookie, flat side down, on top of the filling. Chill for at least 30 minutes before serving.