Adjust an oven rack to the middle position. Preheat the oven to 350 degrees Fahrenheit (175 degrees Celsius). Line 3 baking sheets with parchment paper or silicone baking mats.

In a small bowl, whisk together the flour, baking soda, and salt.

In the bowl of a stand mixer fitted with a paddle attachment, beat the butter on medium speed until creamy. Add the granulated sugar and brown sugar, and beat on medium-high speed until light and fluffy, about 2-3 minutes.

Add the egg, egg yolk, vanilla extract, and water to the butter-sugar mixture, and mix on low speed until combined.

Gradually add the flour mixture to the wet ingredients and mix on low speed until just combined.

Stir in the chopped chocolate chunks until evenly distributed throughout the dough.

Form the dough into 3 1/2-ounce balls (about a heaping 1/3 cup each) and place them on the prepared baking sheets, spaced evenly apart. Place 4 balls on each baking sheet.

Transfer the baking sheets with the dough balls to the freezer and chill for at least 15 minutes before baking.

Place one chilled baking sheet in the preheated oven and bake for 10 minutes, until the cookies are puffed slightly in the center.

Carefully lift the side of the baking sheet up about 4 inches and gently let it drop down against the oven rack, so the edges of the cookies set and the inside falls back down. Repeat this lifting and dropping process a few times to create ridges around the edge of the cookie.

Bake for a total of 14-16 minutes, until the edges are golden brown but the centers are still soft and slightly undercooked.

Remove the baking sheet from the oven and allow the cookies to cool on the baking sheet for 5 minutes before transferring them to a wire rack to cool completely.

Repeat the baking process with the remaining chilled dough balls on the other baking sheets.

Sprinkle with flakey sea salt.