Preheat the oven to 350 degrees F. and adjust the rack to the middle position. Heat the butter in a medium skillet over medium heat. Add the onions and cook, stirring occasionally, until caramelized, about 12 minutes. Stir in the thyme and cook until fragrant, about 45 seconds. Spread the onions evenly in a 10-inch round baking dish (I used an oval). Layer the vegetables over the onions, alternating the squash, zucchini and tomatoes until you've used them all. Cover the dish with unbleached parchment paper and then a piece of foil (this keeps the foil from touching the food as it bakes). Bake for 15 minutes. Remove the parchment and foil. Sprinkle with salt and cheese. Bake for 15 to 20 minutes, until bubbling.