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Preheat the oven to 350 F. Place free-standing baking cups on a baking sheet.
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In a medium bowl, combine the flour, graham cracker crumbs, baking soda, and salt. Set aside.
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In a large bowl, beat the butter and sugar until light and fluffy. Add the eggs and vanilla, mixing until well combined.
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Add the flour mixture and beat until combined.
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Stir in the chocolate chunks.
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Using a small cookie scoop or spoon, scoop 3 spoonfuls of dough into each cup. Press the dough down into cups to create an even layer.
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Bake for 22-24 minutes or until a toothpick inserted in the center comes out clean.
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Let cookies cool for 5 minutes.
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Using a cookie scoop or rounded spoon, gently press in the center of each cookie to create a small crater.
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Let rest while you prepare the ganache.