Preheat your oven to 375°F. Line a 12 muffin well pan or a 6 extra large muffin well pan with paper muffin liners.
In a large mixing bowl, whisk together the whole wheat flour, baking powder, baking soda, cloves, nutmeg, cinnamon and salt.
In a medium bowl, mix together the pumpkin, applesauce and water. Stir in the brown sugar and mix until the sugar has dissolved into the pumpkin.
Mix in the eggs and the vanilla until completely combined.
Make a well in the dry ingredients. Pour the wet mixture into the well and mix until the ingredients are almost completely incorporated into the mixture. Stir in the nuts and chocolate chips until just combined.
Divide the batter evenly between the muffin wells.
Bake in the preheated oven for 15-22 minutes or until a toothpick or cake tester inserted into the middle comes out clean.
Remove and cool completely on a baking rack. Store in a closed container at room temperature for up to 5 days.
Notes
You can sub in raisins or different types of nuts if desired, as long as it's one cup of add-ins.