Make sure all your ingredients are room temperature before beginning. I highly recommend using the scale for your measurements.
Sift flours, baking soda, baking powder and salt into a bowl. Set aside. (You can also mix together with a whisk rather than sifting.)
Using a mixer fitted with a paddle attachment, cream butter and sugars together until very light, about 5 minutes. Add eggs one at a time, mixing well after each addition. Stir in the vanilla.
Reduce speed to low, add dry ingredients and mix until just combined, 5 to 10 seconds. (I added the dry ingredients at about 1 1/2 cups at a time to avoid a major flour blowout, and mixed in the flour – mostly with my spatula – just enough that it wasn’t sitting on top, to avoid over mixing. Once it was all in the bowl, I ran the mixer to combine everything.)
Drop chocolate pieces in and incorporate them without breaking them.
Press plastic wrap against dough and refrigerate for 24 to 36 hours. Dough may be used in batches, and can be refrigerated for up to 72 hours.
Preheat the oven to 350 degrees. Line a baking sheet with parchment paper or a nonstick baking mat.
Using a 3 tbsp cookie scoop, place balls of dough onto the baking sheet, making sure to turn horizontally any chocolate pieces that are poking up; it will make for a more attractive cookie. Sprinkle lightly with sea salt.
Note: The original recipe calls for using a 1/3 cup scoop of dough for a 5-inch cookie. The 3 tbsp scoop will get you 3-inch cookies.
Bake until golden brown but still soft, 15 minutes (18-20 minutes if you're using the 1/3 cup scoop). Transfer the sheet to a wire rack for 10 minutes, then slip the cookies onto another rack to cool a bit more.
Repeat with remaining dough, or reserve dough, refrigerated, for baking remaining batches the next day. Eat warm, with a big napkin.
Serving Size 1 3-inch cookie