Step 1Whisk together the flour, sugar, arrowroot starch, xanthan gum, baking soda and salt in a medium bowl. Add the coconut oil, applesauce and vanilla extract and stir with a spoon until smooth. Fold in the chocolate chips until evenly distributed. Cover with plastic wrap and refrigerate until firm, at least 30 minutes and up to 1 day.
Step 2Meanwhile, heat the oven to 325 degrees. Line 3 large baking sheets with parchment paper (or work in 3 batches).
Step 3Using a measuring tablespoon or 1/2-ounce cookie scoop, drop spoonfuls of dough onto the prepared baking sheets, spacing them 2 inches apart. Using the bottom of a glass, press gently on each dough ball to flatten it into a 1/3-inch-thick round. Repeat with the remaining dough balls.
Step 4Working with one sheet at a time, bake the cookies for 10 minutes, then rotate the pan and bake until golden brown, about 4 minutes longer.
Step 5Let cool completely on the sheets on wire racks, at least 30 minutes. The cookies need to cool completely before handling or they will break.