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1. Adjust oven rack to upper-middle position and heat oven to 400 degrees. Grease 13 by 9-inch baking dish. Heat oil in 12-inch skillet over medium heat until shimmering. Add onions, 1/2 teaspoon salt, and 1/4 teaspoon pepper and cook, stirring frequently, until soft and golden brown, 15 to 20 minutes.
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2. Add garlic and cook until fragrant, about 30 seconds. Add water and cook until nearly evaporated, scraping up any browned bits, about 2 minutes. Off heat, stir in olives; set aside.
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3. Shingle half of tomatoes in even layer in prepared dish. -Shingle half of potatoes over tomatoes and sprinkle 1 teaspoon thyme, 1/2 teaspoon salt, and 1/4 teaspoon pepper over top. Spread onion mixture evenly over potatoes. Shingle remaining potatoes over onions. Shingle remaining tomatoes over potatoes. Sprinkle remaining 1 teaspoon thyme, 1/2 teaspoon salt, and 1/4 teaspoon pepper over top.
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4. Bake, uncovered, for 1 hour. Sprinkle with Gruyere and continue to bake until cheese is browned and bubbly and potatoes are completely tender, 25 to 30 minutes longer. Let cool for 30 minutes. Serve.
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Gratins are layered practically by definition. For our Potato-Tomato Gratin, in which the potato slices gently cook in the juices released by the tomatoes, it's critical that each potato layer adjoin a tomato layer.
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LAYERS FROM TOP TO BOTTOM
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cheese
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tomato
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potato
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onion
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potato
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tomato