Preheat the oven to 350°. Butter a shallow 3-quart baking dish. In a food processor, pulse 1 cup of the flour with the brown sugar, baking powder and salt. Pulse in the butter. Pulse in the granola. Transfer the topping to a bowl.
In a large bowl, toss the apples with the granulated sugar, lemon juice, cinnamon, nutmeg and the remaining 2 tablespoons of flour, then spread in the baking dish. Sprinkle on the topping and bake for 1 hour, or until the topping is golden and the filling is bubbling. Let cool for 20 minutes, then serve.
Make Ahead: Store overnight at room temperature. Reheat before serving.