Whisk your dry ingredients: Grab a big bowl and mix 2 cups flour, 1 tsp cornstarch, 1/2 tsp baking soda, 1/2 tsp baking powder, and 1/2 tsp salt together. Set aside.
Cream butter and sugars: Put 1/2 cup cubed butter, 1/2 cup dark brown sugar, and 1/3 cup granulated sugar in your mixer. Beat 1-2 minutes until it looks fluffy and light.
Add wet ingredients: Mix in 1 egg, 1 egg yolk, and 1 tsp vanilla extract until everything combines well. Scrape the bowl sides with your spatula to get every bit.
Add dry ingredients slowly: Pour in your flour mixture about 1/4 cup at a time. Mix just until the flour disappears. Don't mix too much, or cookies get tough!
Shape and make wells: Use your 2 tablespoon scoop to make dough balls. Press a floured tablespoon back into each one to create a well. Chill the shaped dough for 30 minutes.
Make pecan filling: Put 6 Tbsp butter, 1/3 cup brown sugar, 1/3 cup maple syrup, and 2 cups chopped pecans in your saucepan over medium heat. Let it simmer 2-3 minutes.
Finish the filling: Stir in 1/3 cup heavy cream, 1/2 tsp cinnamon, 1/4 tsp cloves, 1/4 tsp nutmeg, and 1/8 tsp salt to the bubbling mixture. Cook 1-2 minutes, then cool completely.
Fill and bake: Heat oven to 350°F. Spoon 2 tsp cooled filling into each chilled cookie well. Bake 6 cookies per sheet for 10-12 minutes until edges turn golden brown.
Shape and top: While cookies are warm, spin a circular cutter or glass around each one to make perfect circles. Add more filling on top and sprinkle with flaky sea salt.
Cool completely: Leave cookies on the pan for 10 minutes, then move to a wire rack to cool all the way. This lets the filling set up and get gooey. ENJOY!!!