How to Make It
Preheat the oven to 350°. Butter a 14-by-10-by-2-inch (4 quart) baking dish. Layer half of the butternut squash slices in the baking dish, overlapping them slightly, and season with salt and pepper. Cover with half of the potato slices, overlapping them slightly, and season with salt and pepper. Top with half of the tomato slices and season with salt and pepper. Repeat the layering process with the remaining vegetables, seasoning as you go.
In a medium saucepan, combine the cream, garlic, thyme and nutmeg and bring to a boil over moderate heat. Pour the cream evenly over the vegetables. Cover with foil and bake for about 45 minutes, or until the vegetables are tender when pierced with a knife.
Meanwhile, in a small bowl, combine the bread crumbs, Parmesan, parsley and chives. Sprinkle the crumbs evenly over the gratin. Increase the oven temperature to 400° and bake the gratin, uncovered, for 20 to 25 minutes, or until the crust is golden brown. Let rest for 10 minutes before serving.