In a medium bowl, whisk together the all-purpose flour, baking soda, and fine sea salt until well combined. Set aside.

Place the butter in a microwave-safe bowl and heat in 15–20 second bursts until just melted, stirring between bursts. Let it cool for about 5–10 minutes until warm but not hot.

In a large mixing bowl, combine the melted, slightly cooled butter, packed light brown sugar, and granulated sugar. Whisk for 1–2 minutes until thick, glossy, and slightly lighter in color.

Add the egg, egg yolk, and vanilla extract to the sugar mixture. Whisk until fully blended and smooth with no streaks of yolk.

Switch to a spatula or wooden spoon. Add the dry ingredients to the wet mixture in two batches, gently folding just until combined. A few faint streaks of flour are okay; avoid overmixing.

Fold in the semisweet chocolate chips (and chopped walnuts or pecans, if using) until evenly distributed and no dry flour remains. The dough should be soft but able to hold together in a ball.

Cover the bowl with plastic wrap, a lid, or a plate and chill the dough in the refrigerator for at least 30 minutes and up to 1–2 hours. For extra thick and flavorful cookies, chill the dough several hours or overnight.

About 15 minutes before baking, preheat the oven to 350°F (175°C). Line 2 large baking sheets with parchment paper or silicone baking mats.

Scoop the chilled dough into balls using a medium cookie scoop (about 1 1/2 tablespoons each) or a rounded tablespoon. Place dough balls at least 2 inches apart on the prepared baking sheets. Press a few extra chocolate chips on top and sprinkle lightly with flaky sea salt if desired.

Bake one sheet at a time on the middle rack for 10–12 minutes, or until the edges are set and lightly golden while the centers are still soft and slightly puffy. The cookies should look just a bit underbaked in the middle.

Let the cookies cool on the baking sheet for 5–10 minutes to finish setting, then transfer to a wire rack to cool completely. Enjoy warm or at room temperature.