Put the ghee and maple syrup into a large skillet set over high heat and bring to a vigorous boil. Let boil for a full minute and then add the apples, cinnamon, salt, vanilla bean (throw the pod in as well, we'll fish it out later) and lime juice; lower the heat slightly and cook until the apples are softened and the maple syrup is practically completely evaporated, about 5 minutes. Set aside to cool.
In the bowl of your food processor, combine all the ingredients for the crumble and process on pulse until the mixture is just combined, no more. Refrigerate for 15-20 minutes.
Meanwhile, preheat the oven to 375°F and grease a 9” square baking pan with a little bit of ghee or coconut oil and then line it with parchment paper, leaving a bit of an overhang on either side. This simple precaution will allow for easy unmolding later.
With the tip of your fingers, press a little more than half the crumble at the bottom of the prepared pan. You might want to slightly wet your hands to prevent the mixture from sticking to your fingers. Then, flatten it with a rubber spatula or better yet, a plastic dough scraper if you have one.
Now drop the apple mixture over the base (don't forget to remove that vanilla pod!) and spread it all the way to the edge, then scatter the rest of the crumble mixture right on top, followed by the maple flakes, if using.
Bake for 28 to 30 minutes, until the top gets nice and golden brown and the house is filled with the most delicious smell.
Remove from the oven and allow to cool to room temperature, then transfer to the refrigerator to chill completely. Remove from the pan and cut into 12 squares.