Mill the soft wheat berries as finely as possible. Let the flour cool completely if it feels warm.
In a medium bowl, whisk together the soft milled wheat flour, baking soda, baking powder, and salt. Set aside.
In a large mixing bowl, cream the softened butter, brown sugar, and granulated sugar together for about 2 minutes.
Add the egg, egg yolk, and vanilla extract. Mix until smooth.
Add the dry ingredients to the wet ingredients and mix just until combined.
Fold in the chocolate chips.
Let the dough rest for 20 minutes.
Scoop the dough into tall mounds, about 2 tablespoons each. Do not flatten.
Chill the scooped dough for at least 1 hour. For thicker cookies, chill for 2 to 4 hours.
Preheat the oven to 350°F.
Place the chilled cookie dough balls on a parchment-lined baking sheet, leaving space between each one.
Bake for 10 to 12 minutes, or until the edges are set and lightly golden and the centers still look slightly soft.
Let the cookies cool on the baking sheet for 10 minutes before moving them to a cooling rack.