Line a baking sheet with parchment paper or a Silpat. Set aside.
Add the butter to a skillet set over medium-low heat. Melt the butter and cook until the milk solids caramelize and the butter turns golden brown, approx. 5-8 minutes. Set aside to cool to room temperature.
In the bowl of a stand mixer fitted with a paddle attachment, combine the butter and sugars. Mix until well combined. The mixture will be thick like wet sand. Add the eggs and the vanilla and mix until fully incorporated and the mixture has lightened in color.
In a separate bowl, combine the flour, baking soda, baking powder, and salt. Whisk to combine. Add the flour mixture to the butter/sugar mixture, mixing until just combined. Stir in the chocolate chips.
Using a 3-tablespoon cookie scoop, portion the dough onto the baking sheet, 6 cookies per baking sheet. Press extra chocolate chips into the dough if desired. Chill for 15-20 minutes. (Note 1)
Preheat oven to 350 degrees.
Bake the cookies for 11-12 minutes until golden brown around the edges and just set in the middle. Sprinkle with flaky sea salt. Let cool for 3-5 minutes on the baking sheet before transferring to a cooling rack. Store in an airtight container.
To save room in the refrigerator, portion all of the dough out onto one baking sheet. Chill. To bake, transfer 6 balls of dough to a separate baking sheet. Repeat with remaining batches.
Chilling cookie dough is an important step, so don't skimp on the chilling time specified in a recipe. Chilling the dough chills the butter which prevents the cookies from over-spreading during baking. If the butter is too warm, the cookies will spread too much. Chilling the dough also allows for the ingredients to meld and the flavors to enhance.
To freeze cookie dough, portion the dough using a cookie scoop and place on a parchment-lined baking sheet. Put the pan in the freezer to flash-freeze the dough until firm. Then, transfer the dough balls to a freezer-safe bag and store for up to 3 months.
To bake frozen dough: place the dough balls on a parchment-lined baking sheet and bake according to the recipe's directions, allowing an extra 1-2 minutes of baking time.
To freeze cookies: allow the cookies to cool completely. Place on a parchment-lined sheet pan in a single layer and freeze until firm. Transfer to a freezer-safe bag or container and store in the freezer for up to 1 month. To eat, let the cookies thaw at room temperature or warm briefly in the microwave.
For storing: to keep the cookies chewy, store a slice of bread in the container with the cookies. The moisture in the bread keeps the cookies soft. The bread will dry out and can be discarded.