Preheat the oven to 375 degrees F. Line three baking pans with parchment paper and set aside.
Whisk the flours, cocoa powder, baking powder, salt and xanthan gum together in a medium bowl.
Put the sugar, applesauce, coconut oil, grapeseed oil and vinegar in a large bowl and beat with an electric mixer on low speed until combined, about 1 minute. Add the flour mixture to the bowl with the wet ingredients, alternating with 1/3 cup water, until fully combined. Fold in the chocolate chips.
Spoon heaping tablespoons (or a small scoop) of the dough onto the baking sheets, 1 inch to 1 1/2 inches apart. Bake the cookies in two batches, two sheets at a time, until the cookies are set and beginning to crack on the top, 16 to 18 minutes. Rotate the sheets halfway through for even baking.
Remove from the oven and let the cookies cool on the sheets for 2 minutes, and then remove to a rack and cool completely. Bake the remaining cookies on the third pan following the above directions.
Vegan Cinnamon and Pecan Cookies: Make the Vegan Chocolate Cookies, adding 1 1/2 teaspoons ground cinnamon to the flour mixture, and folding in 1 cup chopped pecans. Bake as directed. Vegan Chocolate Peanut Butter Cookies: Make the Vegan Chocolate Cookies, adding 1/3 cup natural peanut butter to the wet ingredients, and increasing the water to 2/3 cup. Substitute in 3/4 cup chopped roasted unsalted peanuts in place of the chocolate chips in the recipe. Vegan Rocky Road Chocolate Whoopie Pie Cookies: Make the Vegan Chocolate Cookies. Reduce the vegan chocolate chips to 3/4 cup and fold in 3/4 cup chopped raw almonds. When cool place 3 mini vegan marshmallows on each of 18 overturned cookies, and broil 1 minute. Top each with another cookie to make sandwiches.
From Food Network Kitchens