Preheat the oven to 350 degrees.
Gently saute the onions and thyme in the oil for about 20 minutes, or until the onions are soft and golden. Meanwhile, toss the apple slices with the flour. In a separate bowl, combine the cheese with the bread crumbs.
Oil a baking dish, approximately 8 by 8 by 3 inches, and layer the ingredients as follows: the squash, with a sprinkling of salt and pepper; the sauteed onions; the apple slices, with a bit more salt and pepper; and finally the Cheddar–bread crumb mixture.
Bake covered for 30 minutes, then uncovered for 15 minutes, or until the apples are tender and the topping bubbly and golden. Note: To prepare squash for this dish, peel the squash, remove the seeds, cut into slices or cubes, steam until tender, then mash.
Recipe compliments of Thyme in the Garden (www.athymeinthegarden. com). This dish will be featured in their Autumn Harvest: Comfort Foods class on October 26.