In a medium bowl, combine oats, all-purpose flour, whole wheat flour, flaxseed, baking powder and baking soda.
In a large mixing bowl, beat butter with an electric mixer for 30 seconds. Beat in the brown sugar and applesauce until combined. Beat in eggs and vanilla.
Beat in as much of the flour mixture as you can with the mixer. Stir in any remaining flour. Stir in chocolate and dried fruit.
Drop dough by tablespoonfuls 2 inches apart onto cookie sheet. Flatten slightly, if you like. Bake in a 375 degree F oven for 8 to 10 minutes or until edges are light brown. Remove; cool on wire racks. Makes 6 dozen cookies.