Salted Chocolate Fudge Peanut Butter Cookies

In a large bowl, beat the butter, peanut butter and sugar together until smooth. Add in the egg and vanilla and beat again until smooth.
Melt the semi-sweet chocolate chips in the microwave, about 1 minute. Allow chocolate to cool a bit, and then beat it into the cookie dough mixture until completely combined.
In a medium bowl, whisk together the flour, cocoa powder, baking soda and sea salt. Add the dry ingredients to the wet ingredients and mix until completely combined. Add in the milk chocolate chips and stir them into the dough with a rubber spatula until they are evenly distributed.
Wrap the top of the dough bowl with plastic wrap and refrigerate for at least 4 hours. I put mine in the fridge overnight.
When ready to bake, preheat oven to 350 F and line a baking sheet with a Silpat mat or parchment paper.
Place dough mounds on prepared baking sheet in tablespoonfuls spaced at least 2 inches apart. If you notice the dough seems super hard right out of the fridge, this is OK!
Bake for about 10 minutes, or until edges and tops of the cookies are just set. (Pull them out even if they look slightly under-cooked! The cookies will firm up as they cool.) Right out of the oven, sprinkle the tops of the cookies with a bit of flaked sea salt.
Allow cookies to cool on baking sheet for about 10 minutes. When the cookies are cooled enough and not floppy, transfer them to a cooling rack. Repeat with the rest of the dough.