From Kim Boyce’s cookbook Good to the Grain, via http://www.leciawphinney.com/2010/09/what-i-can-do.html.
Dry Mix
3 cups whole-wheat flour
1 1/2 tsp. baking powder
1 tsp. baking soda
1 1/2 tsp. kosher salt
Wet Mix
8 oz. cold unsalted butter, cut into 1/2 pieces
1 cup dark brown sugar
1 cup granulated sugar
2 eggs
2 tsp. vanilla extract
8 oz. bitter sweet chocolate, roughly chopped into 1/4" - 1/2" chunks
Preheat oven at 350.
For cookies: Line two baking sheets with parchment paper.
For cookie bars: Butter a 9" x 13" baking dish.
Mix dry ingredients into a large bowl, preferably after sifting.
Mix butter and sugars using a stand mixer with paddle attachment at low speed. When butter and sugar are just blended, add eggs one at a time followed by vanilla.
Add flour and mix until barely combined, about 30 seconds. Add chocolate and mix until pieces are evenly distributed.
For cookies: Make 3 Tbsp balls and place on baking sheets with 3 inches between each pair of cookies. Bake 16-20 minutes.
For cookie bars: Spread dough evenly in the baking dish, and bake until a toothpick inserted in the center comes out clean.
We usually make these as cookie bars. 12 oz of chocolate chips can work in place of the chopped dark chocolate.