Step 1: Preheat oven to 350 degrees F.
Step 2: Line two cookie sheets with parchment paper.
Step 3: In medium mixing bowl, beat margarine, maple syrup, and applesauce until smooth and creamy.
Step 4: Add the rest of wet ingredients and mix well. In separate bowl, whisk together flours, baking powder and soda, flax, salt, and arrowroot.
Step 5: Mix wet into dry ingredients until well combined. Fold in chocolate chips and stir well.
Step 6: Drop spoonfuls onto prepared cookie sheet and using wet fingertips, press down each cookie evenly (continue to dip fingers in water to prevent sticking). The cookies will not spread much, so you can put them close together on the cookie sheet.
Step 7: Bake for 18 to 20 minutes, or until lightly browned.
Step 8: Remove from oven and cool cookies on a wire rack.
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