In a small saucepan set over medium heat, melt the butter. Swirling the pan occasionally, continue to cook the butter. It should become foamy with audible cracking and popping noises.

Once the crackling stops, continue to swirl the pan until the butter develops a nutty aroma and brown bits start to form at the bottom. When the bits are amber in color, about 2 to 3 minutes after the popping stops, remove from heat and pour into a mixing bowl.

Add in the sugars, stir, then set aside to cool completely.

In a medium or large bowl, combine the flours, baking soda, baking powder, and salt.

Add the eggs, egg yolk, and vanilla to the browned butter mixture, and stir with a rubber spatula until combined. Slowly stir in the flour mixture until just combined. Stir in the chocolate chips and wafers.

Wrap the dough in plastic wrap and refrigerate for at least 24 hours but no more than 72 hours. Let the dough sit at room temperature until just soft enough to scoop.

Meanwhile, preheat oven to 350ºF. Line baking sheets with parchment paper.

Divide the dough into 3-tablespoon sized balls using a cookie scoop and drop onto prepared baking sheets, leaving about 3 inches between each piece of dough to spread.

Bake for 11 to 13 minutes, or until golden brown. Sprinkle with flaky sea salt, if desired. Let cool for 5 minutes before removing to wire racks to cool completely.