Brown the butter over medium heat. Stir the butter constantly until it begins to foam and turn a golden color. Make sure not to brown the butter to much or it will taste burned and make the cookie dry.
In a large mixing bowl, whisk together the cooled butter, brown sugar, white sugar, and pumpkin butter.
Add the egg, egg yolk, and vanilla extract and mix until everything is incorporated.
Slowly add in the dy ingredients (flour, baking soda, salt). Make sure not to overmix. Fold in the chopped chocolate.
Refrigerate the cookie dough for 30 minutes.
Preheat the oven to 350F and line a cookie sheet with parchment paper. Use an ice-cream scoop to scoop the dough into balls. Place them 2 inches apart on the sheet. Sprinkle flaky sea salt on top of each cookie.
After the cookies have been in the oven for 4 minutes, open the oven door and bang the cookie pan to force the dough to spread out. Return the cookies back to the oven for 3 more minutes and repeat. Then leave them in for 4 more minutes or until golden brown and the center is still gooey. (11 minutes total)