In a stand mixer, cream the butter, brown sugar, and white sugar together until light and fluffy. Add vanilla extract.
Add eggs one at a time, and beat until well incorporated.
Whisk together the cocoa, flour, baking soda, and salt. Sift.
Add sifted ingredients to the mixing bowl. Use a wooden spoon to fold the dry ingredients in until they're just combined. For the longest time, it will feel like you're just moving around the sifted ingredients. Suddenly, it will feel like you're trying to stir cement. This is what you want.
Stir in the chocolate chips and the chopped pecans. Mix just enough to distribute. Don't overwork the dough!
Cover the dough with plastic wrap and refrigerate for an hour or so.
Preheat the oven to 350 and line a cookie sheet with parchment paper.
Dip a small scoop into water (to prevent sticking) and drop dough onto a cookie sheet about 1 1/2 inches apart. Flatten the balls slightly, and top each with a square of chocolate and a pecan half.
Bake for 15 to 20 minutes or until the edges begin to brown (less if using a thinner metal cookie sheet, so watch them carefully starting around 10 minutes). Allow the cookies to cool on the cookie sheet. I don't know why, but that helps them to be moist and gooey.