Preheat the oven to 400°F and grease an 8x8-inch baking dish.
Make the filling: Combine the apples, apple cider vinegar, and water in a saucepan and simmer over very low heat, covered, stirring occasionally (making sure the apples don’t burn on the bottom of the pan) for 15 minutes. Uncover, stir, and add the cinnamon, ginger, nutmeg, and salt and stir again. The apples should be tender, and the juices should be thick.
Make the topping: In a food processor, place the flours, oats, walnuts, sugar, coconut oil, cinnamon, and salt and pulse until crumbly. Add the water if needed.
Scoop the apple filling into the baking dish and sprinkle with the topping. Bake for 18 to 22 minutes or until lightly crisp on top.