Preheat the oven to 350°F. Spray two 24 mini-muffin tin with nonstick cooking spray.

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

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. Once the bits are amber in color, about 2 to 3 minutes after the popping stops, remove from heat and pour into a mixing bowl.

While the butter is still hot, stir in the granulated sugar and brown sugar. Let cool before adding in the vanilla and the eggs and yolk, one at a time, stirring well after each addition. Stir in the flour mixture until just combined.

Press a 1-tablespoon sized ball of dough into each muffin cup. Bake for 12 to 15 minutes, or until golden brown. Remove from oven and using the end of a wooden spoon, make 1-inch wide indentations into the center of each cookie.

Spoon a teaspoon of dulce de leche into each indentation. Sprinkle with sea salt. Let cool completely before serving.