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Preheat the oven to 350° F and line cookie sheets with parchment paper, silicone mats, or spray with cooking spray.
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In a small bowl, combine the flour, cocoa, baking soda, and salt. In a large bowl, use an electric mixer to beat together sugars, butter, and vanilla. Add the eggs, one at a time. Then gradually stir in the flour/cocoa mixture. Fold in the chocolate chunks (save a few for putting on top after they come out of the oven if desired).
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Use a cookie dough scoop or tablespoon to scoop balls of cookie dough onto the prepared baking sheets. Flatten each ball slightly, and place an unwrapped caramel on top. Then, using about two more scoops of cookie dough, cover the caramel completely and press the edges of the dough to make sure it’s sealed inside.
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Bake for about 10 minutes. Top with additional chocolate chunks and a sprinkle of sea salt, if desired. Let the cookies cool for about 10 minutes before serving. Enjoy!