Preheat oven to 350°F and line a cookie sheet with parchment paper or a silpat.

Make the flax egg and set aside to thicken.

Meanwhile, combine flours, baking powder, baking soda, salt and spices in a medium bowl. Whisk until combined.

Add all the wet ingredients including the flax egg to a large bowl and whisk until fully combined and smooth.

Dump the dry ingredients into the wet ingredients and stir until all the flour is incorporated.

Fold in the chocolate chips.

Drop heaping spoonfuls of the batter on a cookie sheet about 1 inch apart. Optionally, top with additional chocolate chips and a sprinkle of coarse sea salt, gently pressing the cookies down a but to form more of a traditional cookie shape since they won't spread too much while baking.

Bake for approximately 14-16 minutes, until the edges start to brown and the cookie is set but still soft to the touch.

Remove from oven and let cool for 10 minutes on the baking sheet before transferring each cookie to a cooling rack.

Store on the counter for 3-4 days in a container for softer cookies or keep chilled in the refrigerator for up to 5 days for a firmer texture.