Combine Dry Ingredients: In a medium bowl, whisk together the gluten-free 1-to-1 flour, Dutch-processed cocoa powder, baking soda, and fine sea salt. Whisking thoroughly ensures the leavening and salt are evenly distributed and helps to aerate the flour and cocoa. Set aside.

Melt Chocolate and Butter: Create a double boiler by placing a heatproof bowl over a saucepan of simmering water (make sure the bottom of the bowl does not touch the water). Add the 4 ounces of chopped bittersweet chocolate and the ½ cup of butter to the bowl. Stir occasionally until both are completely melted and the mixture is smooth and glossy. Remove the bowl from the heat and set aside to cool slightly for about 5 minutes.

Whisk in Sugars and Eggs: Pour the slightly cooled chocolate-butter mixture into a large mixing bowl. Add the light brown sugar and granulated sugar and whisk vigorously for about a minute until the mixture is well combined and no lumps of sugar remain.

Add Eggs and Vanilla: Add the room temperature egg and the extra egg yolk, along with the vanilla extract. Whisk vigorously for another full minute. The mixture should become thick, glossy, and smooth. This step helps to emulsify the fats and sugars, creating that signature shiny, crackly top on the cookies.

Combine Wet and Dry: Pour the dry ingredient mixture into the wet ingredients. Use a rubber spatula to fold everything together until just combined. The dough will be soft and seem a bit oily. Be careful not to overmix; stop as soon as you no longer see streaks of flour.

Fold in Chocolate Chips: Gently fold in the 1 ½ cups of chocolate chips or chunks until they are evenly distributed throughout the dough.

The Critical Chill: Cover the bowl tightly with plastic wrap and refrigerate the dough for at least 3 hours, or preferably overnight (up to 48 hours). Do not skip this step. This is essential for managing spread, developing flavor, and ensuring a non-gritty texture.

Preheat and Prepare for Baking: When you’re ready to bake, preheat your oven to 350°F (175°C). Line two large baking sheets with parchment paper.

Scoop and Bake: Using a medium-sized (1.5 to 2-tablespoon) cookie scoop, portion the cold dough into balls and place them on the prepared baking sheets, leaving at least 2-3 inches of space between each cookie to allow for some spreading.

Add Toppings (Optional but Recommended): For that bakery-style look, gently press a few extra chocolate chips or chunks onto the tops of the dough balls.

Bake: Bake for 11-13 minutes. The edges of the cookies should be set, but the centers will look soft, puffy, and slightly underdone. This is the key to a fudgy center.

The Final Touches: Remove the baking sheets from the oven. Immediately sprinkle the tops of the hot cookies with a little flaky sea salt. Let the cookies cool on the baking sheet for 10 minutes. During this time, they will continue to cook from the residual heat and will set up. After 10 minutes, carefully transfer the cookies to a wire rack to cool completely.