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Preheat oven to 325 degrees. Brush 3 dozen mini-muffin pans with oil; set aside.
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In a medium bowl, whisk together flour, potato starch, arrowroot, sugar, baking powder, baking soda, xanthan gum, salt, and unsweetened cocoa powder; set aside. In a large bowl, mix together applesauce, 1/2 cup canola oil, and vanilla. Slowly add flour mixture, stirring to combine. Stir in coffee until it forms a batter. Fold in chocolate chips.
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Place 1 tablespoon batter into each prepared muffin cup. Transfer muffin pans to oven, and bake until a toothpick inserted into the center comes out clean, 12 to 15 minutes. Let cool completely on a wire rack before unmolding.