Make the brown butter. In a small saucepan over medium-low heat, melt the butter, stirring occasionally. Continue cooking for 3-5 minutes, until the bubbler bubbles, foams and the milk solids start to separate. The solids will start to smell nutty and turn a deep amber color. Remove it from the heat and pour it into a medium bowl to cool slightly.
Mix the flour, baking soda, baking powder, and 1 teaspoon of salt in a medium bowl.
In the bowl of a stand mixer fitted with the paddle attachment or in a large bowl with an electric mixer, beat the butter, brown sugar and granulated sugar together until combined, 2-3 minutes.
Add the vanilla, egg and egg yolk and continue to beat until combined, about 1 minute.
With the mixer running on low speed, slowly add the drygredients, then turn the speed up to medium-high to combine. Stop to scrape down the bowl as needed.
Stir in the chocolate chips and chocolate chunks. Cover with plastic wrap and refrigerate for at least 3 hours, or ideally overnight. You can leave it in the fridge for up to 72 hours. See notes for freezing.
When you're ready to bake preheat the oven to 350°F. Line two large baking sheets with parchment paper. Use a large cookie scoop to scoop the dough out onto the cookie sheets. You should have 24-28 scoops. Place a caramel in the center of a dough ball then cover it with another. Pinch the seams to close the caramel inside and roll the ball into a balls just slightly taller than it is round. See blog post images for an example. Repeat with the remaining dough. You should have 12-14 large cookies.
Arrange the cookie dough on the secon d cookie sheet a few inches apart. Bake for 10-13 minutes, until the edges and tops of just set and slightly golden brown. Press a few additional chocolate into the top of the baked cookies and sprinkle with flaky sea salt. Cool on the baking sheet for 5 minutes then transfer to a wire rack to cool completely.