Preheat oven to 350°F. Line several baking sheets with parchment paper, although these cookies do not stick to the pan and you could easily skip this step.
In a bowl, sift together the flours, flax seed, salt, and baking soda. Set aside.
In the bowl of a stand mixer with the paddle attachment, or with a hand mixer, cream together the butter and peanut butter until light and fluffy. Add the sugars and honey and beat on high for three minutes, scraping down the sides of the bowl as needed. Add the egg and vanilla, then mix on medium speed until well blended. Add the dry ingredients to the bowl and stir to just combine.
Using about one tablespoon of batter per cookie, form the batter into small balls. Roll each ball in granulated sugar and place on the prepared baking sheet, about two inches apart. Bake the cookies at 350°F until they begin to crack, about 10-15 minutes. At this point, top each cookie with a piece of dark chocolate, pressing slightly to seat the chocolate. Bake an additional three minutes. Remove and cool on a wire rack.
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