Preheat oven to 350 degrees F (175 degrees C). Grease a large bar-cookie pan.
Stir pumpkin puree, eggs, sugar, oil, and water together in a large bowl until smooth.
Stir all-purpose flour, pastry flour, powdered milk, almonds, flax seed meal, baking soda, salt, cinnamon, nutmeg, cloves, and ginger together with a whisk in a separate bowl; stir into the pumpkin mixture until you have a smooth batter. Pour the batter into the prepared pan. Sprinkle chocolate chips over the top of the batter.
Bake in the preheated oven until a toothpick inserted into the center comes out clean, about 30 minutes. Let cool completely before cutting.