Preheat the oven to 350 degrees F. Place the phyllo shells on a baking sheet and bake until crisp, about 5 minutes. Remove from the oven (keep the oven on) and let cool.
For the filling: Meanwhile, melt the butter in a large skillet over medium heat. Add the apples, cinnamon, nutmeg, salt and lemon juice. Cook, stirring often, until the apples start to soften and release some juices, about 4 minutes. Add the sugar and continue to cook, stirring often, until the sugar has dissolved, about 2 minutes more.
Stir together the cornstarch and 2 tablespoons of water in a small bowl. Stir into the apple mixture and cook, stirring often, until the liquid is very thick, about 2 minutes more. Stir in the vanilla, remove from the heat and set aside.
For the granola crisp topping: Line a baking sheet with parchment paper. Stir together the oats, flour, sugar, cinnamon, salt, butter and honey and spread the mixture on the baking sheet, using your hands to form some small clumps. Bake until browned and crisp, about 10 minutes. Remove from the oven, stir in the almonds and let cool.
To assemble, add a heaping tablespoon of the filling to each phyllo shell, followed by a tablespoon of the topping. Serve warm or at room temperature.