Preheat the oven to 320 Fahrenheit/160 Celsius
Slice the onion into ribbons. Finely chop the shallot. Place a medium skillet over medium heat. Drizzle 1-2 tablespoons into the pan after it warms, and then add the alliums (onions and shallot). Cook for about 10 minutes until cooked down and nearing translucency. Season with fleur de sel.
Choose your baking dish - oven-safe - in a diameter that you wish to serve. Place the onions after they have been sautéed into the bottom of the baking dish.
Slice the tomatoes, courgettes and aubergines in small rounds, all the same thickness. If the aubergines or tomatoes are too large in diameter, cut the bottom flat so that the top 2/3 can match the other vegetables.
Arrange the vegetables, alternating tomato, courgette and aubergine, and in the same order as you move around the baking dish until it is filled. You can stack in like a deck of cards or fan out. If you are including cheese, include the cheese slices (same in size and thickness as the vegetables) in the order of stacking. Sprinkle with Herbes de Provence. Now season with salt and pepper, drizzle with olive oil (this is when you can drizzle tomato sauce over the vegetables (in between the slices or simply resting on top of the onions before you start stacking).
Bake at the low heat of 320 F/160 C for 90 minutes. Cover with tin foil for the first hour. Check and see how the vegetables are cooking. The tenderness of the eggplant will determine how much longer to cook the dish. After one hour, remove the tinfoil, sprinkle fresh parmesan on top of the vegetables and bake for the remaining 20-30 minutes until done.
Serve warm and immediately. Garnish with fresh basil and enjoy!