Melt the 1 cup (225g) butter in a light-colored saucepan over medium heat, swirling often, until the milk solids turn amber and smell nutty, about 5 to 7 minutes. Pour into a large bowl and cool for 20 minutes.

Whisk the 1 cup (200g) dark brown sugar and 1/2 cup (100g) granulated sugar into the cooled butter for 2 minutes, then add the 2 eggs, 1 yolk, and 2 tsp vanilla extract and whisk for another 60 seconds until glossy.

Fold in the 2 1/4 cups (280g) flour, 1 tsp baking soda, and 1 tsp fine sea salt with a spatula until just combined, about 20 to 25 folds.

Fold in the 2 cups (340g) chocolate chips, cover, and refrigerate for at least 1 hour.

Heat the oven to 375°F (190°C) and line 2 baking sheets with parchment. Scoop dough into 3 oz (85g) portions, space 3 inches apart, and bake 13 to 15 minutes until edges are golden and centers look just set.

Rest on the pan for 5 minutes, transfer to a wire rack, and finish with a pinch of flaky sea salt over each warm cookie.