Preheat your oven to 425°FPlace the butternut squash, apples, onion and cranberries in a large mixing bowl.In a seperate container, such as a glass measuring cup, mix the melted ghee, rosemary, thyme, salt and pepper.Pour this right over the reserved vegetables and mix well with your hands, until all the pieces are evenly coated.Line a 13" x 18" baking sheet with parchment paper and then spread the butternut squash mixture into a single layer.Bake on the top rack of the oven for about 30 minutes, or until the apples and squash start to caramelize on the edges.Meanwhile, make the cooking liquid and crumble. For the cooking liquid, simply whisk all the ingredients together in a glass measuring cup. For the crumble, place all the ingredients in a small mixing bowl and then mix well with your fingers, making sure that all the ingredients are well combined.After 30 minutes, take the squash and apple out of the oven and transfer to a square baking dish. Pour in cooking liquid and top with the crumble.Return the casserole to the oven, on the middle rack this time, and cook for an additional 15 minutes, until the liquid bubbles up on the sides and the crumble turns beautifully golden brownRemove from the oven and allow to rest for 15 minutes before serving.