In a large mixing bowl, stir together all-purpose flour, sugar, baking powder, baking soda, salt, cocoa powder, and chocolate pudding mix. Make a well and add the Amish Friendship Bread Starter, oil (and applesauce, if using), milk, eggs and vanilla extract; mix well. Stir in about 1/2 cup chocolate chips. Pour batter into prepared pans. Sprinkle chocolate chips on top of each cupcake (optional).