Pour the apple cider into a small sauce pan and add the cinnamon sticks and whole cloves. Bring to a low boil over med-high heat. Then turn to low and simmer for 15-20 minutes,, stirring occasionally, until cider is reduced to half, leaving about 1 cup. Remove from heat, strain to remove cinnamon sticks and cloves, and allow to cool.
Prehead oven to 350° F. Spray two donut pans (6 donuts each) with non-stick pan spray.
In a large bowl, mix together the all-purpose flour, whole wheat pastry flour, ground flax seed, baking powder, cinnamon, nutmeg, cloves, ginger, cardamom, and salt.
In a separate mixing bowl, blend together the brown sugar, egg, vegetable oil, melted butter, and reduced apple cider. Make a well in the dry ingredients and pour the blended liquid ingredients into the dry. Stir until evenly moistened.
Spoon batter into a zippered plastic bag and press closed. Snip off a small corner of the bag and squeezing gently, pipe the batter into the prepared donut pan.
Place pans in preheated oven and bake for 10-12 minutes until toothpick inserted into donuts comes out clean or with just a few crumbs sticking to it. Do not overbake. Remove from oven when done and let cool in pans for 5 minutes.
If cinnamon sugar topping is desired, mix together the ½ c. granulated sugar and 2 tsp. cinnamon. Remove donuts from pan after 5 minutes, while still warm, and dip into the cinnamon sugar mixture. Place on wired rack and serve immediately.