In a large mixing bowl, combine the flour, baking soda, baking powder, and salt. Whisk to combine. Set aside.
In the bowl of a stand mixer fitted with a paddle attachment, cream together the butter and sugars until well combined, about 2 minutes. Add in the egg, egg yolk and vanilla and mix until well combined and lightened in color.
Slowly add in the flour mixture and mix until just combined. Stir in the dark chocolate chips, ½ cup chopped chocolate, and the chopped pecans. Chill the dough for 30 minutes.
Preheat the oven to 350 degrees. Line a baking sheet with parchment paper.
Using a 2-tablespoon cookie scoop, portion the dough onto the baking sheet Flatten slightly and top each dough ball with extra chopped chocolate and pecans. Bake for 9-11 minutes until lightly browned around the edges. The middle will look slightly underdone. Remove from the oven. Top each cookie with flaky salt, if desired. Let cool on the baking sheet for 5 minutes before transferring to a cooling rack. Store in an airtight container.
Use room temperature butter and eggs. Room temperature ingredients incorporate together more completely.
Add a mixture of chocolate chips and chopped chocolate for the ultimate chocolate factor.
Chill the cookie dough to help prevent the dough from spreading during baking.
Use a cookie scoop to ensure the cookies are all the same size for even baking.
Line the sheet pan with parchment paper or a silicone baking mat. This helps to prevent the cookies from spreading and lends to easy clean-up.
Before baking, top the cookies with extra chocolate and pecans for the fresh-from-the-bakery-look.
After baking, top the cookies with flaky sea salt for the ultimate treat.
The cookie dough can be made ahead of time. It's best when chilled for at least 30 minutes, or up to 3-4 days. Make the dough one day, bake the cookies the next.
This cookie dough freezes beautifully. Instead of chilling the dough, use a cookie scoop to portion the dough onto a parchment-lined sheet pan. Freeze until firm. Then transfer the dough to a zipper-top bag and store for up to 3 months. Bake from frozen, allowing an extra 2-4 minutes of baking time.
To freeze the cookies after baking, allow the cookies to cool completely. Freeze until firm. Then transfer the cookies to a zipper-top plastic bag, layering parchment paper in between the cookies. Freeze for up to one month. Thaw and serve.