Preheat your oven to 350°F. Grease and line a cookie sheet.
In a large bowl, combine the butter and sugars together with a hand mixer (or use a stand mixer with the paddle attachment if you have one). Beat for 2-3 minutes until light and fluffy. Add the cocoa powder and beat until totally incorporated.
In a separate medium bowl, add the flour, salt, baking soda, and baking powder. Whisk to combine, then add this to the butter mixture in the other bowl. Beat until no streaks of flour remain.
Using a cookie scoop (or your hands) scoop tablespoon-sized balls of cookie dough and press an indent into the center with your fingers. Place 12 per baking sheet and bake for 12 minutes.
When the cookies come out of the oven, use a spoon to press the indent in further, the cookies rise in the oven so you need to make sure you have a good sized indent.
Allow to cool before adding caramel-pecan and chocolate toppings.
For the Caramel:
In a large heavy bottomed saucepan, add the sugar. Put it over medium-low heat until you see the sugar begin to melt. When the sugar starts to liquefy, swirl it a bit to distribute the heat evenly. Try not to stir the caramel. Be patient, it will all work out. Once it reaches a nice amber color, add the heavy cream and whisk until combined. It will bubble and sieze at first but keep stirring, it will smooth out. Add the butter and stir to incorporate. Set aside to cool.
For the Pecans:
Chop 1 cup of pecans and toast them for 1 minute in a pan on the stove. When they become fragrent, take them off the heat and pour them into the caramel sauce. Stir to combine.
For Assembly:
Once the cookies are cooled, spoon the pecan caramel mixture into the thumbprints in the cookies. Drizzle with melted dark chocolate and top with flaky salt. Enjoy!