Preheat oven to 375 degrees F.
In a large bowl, toss butternut, onion, garlic, salt, pepper, cinnamon, nutmeg, fresh ginger and olive oil. Coat squash and onions completely.
Pour mixture into a glass or ceramic baking dish (or cast iron skillet). Cover with foil and bake for 20 minutes.
In a separate bowl, combine apples, maple syrup, vinegar and fresh thyme. Arrange apple mixture over the squash. Re-cover with foil and bake for another 10 minutes.
Uncover the dish, stir and bake for about another 20 minutes, stirring every 10 minutes, until the squash is fully cooked and the liquid is absorbed. Taste and adjust the seasoning.
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