Preheat the oven to 350℉. Line two baking sheets with parchment paper or a silicon baking mat. Set aside.
In a food processor, pulse the pistachios until mostly broken up. There should still be some small chunks and it shouldn't be as fine as almond flour. Set aside.
In a medium sized saucepan, melt the butter over medium heat. Once melted, it will begin to sizzle. Keep cooking, stirring frequently, until you see brown specks. As soon as you do, add the ground up pistachios. Keep cooking, stirring frequently, until the nuts begin to toast and brown, roughly 2 more minutes. Pour the mixture into a large heat safe mixing bowl. Let the mixture cool for 5 minutes before continuing.
Add the brown sugar, granulated sugar, and honey to the pistachio mixture, and whisk to combine. Add the egg yolk, vanilla, pistachio extract, and milk and whisk to combine. Sift in the flour, baking soda, cinnamon, and salt, and use a spatula to fold it together. Mix in the chopped chocolate. The dough will be a little greasy.
Using a cookie scoop or your hands, roll the dough into balls, roughly 1-2 Tablespoons in size. Place 3 inches apart on the previously prepared baking sheet. Bake for 10-12 minutes or until the cookies are browned on the outside but just a little gooey in the center. Sprinkle with flakey sea salt and enjoy warm!
Cookies stay fresh sealed in an airtight container at room temperature for up to 5 days.