1. In the bowl of a stand mixer, combine the softened butter and sugars. Beat for a few minutes or until they are fluffy, lightened in color, and completely combined.
2. Add in the eggs and vanilla and beat until combined.
3. While the wet ingredients are creaming together, mix the flours, salt, spices, baking soda, flaxseed, and oats in a large mixing bowl until well combined.
4. Add all the dry ingredients into the wet ingredients and mix until just incorporated.
5. Stir in the chocolate by hand.
6. At this point, you can bake the cookies, or you can refrigerate the dough until you need it.

To Bake:

1. If using cold cookie dough, remove it from the fridge at least 30 minutes before you want to bake (I like to let it return to room temperature – if I have the time, I let it sit out for an hour before forming into balls and baking).
2. Preheat the oven to 350°F and line baking sheets with parchment paper.
3. Scoop out 2-tablespoon balls of the dough and place on the baking sheets, leaving a couple inches of space between the dough balls.
4. Bake for 10-13 minutes or until the edges of the cookies are golden and the centers are mostly set. I prefer to bake these to the point of the centers still looking SLIGHTLY underdone and a little bit puffy. They will continue to cook on the baking sheet as they cool and will be chewier if you underbake them just slightly.
5. Cool on the sheets for 5 minutes before transferring them to cooling racks to finish cooling.
6. Store cooled cookies in an airtight container for up to 3 days.