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Preheat the oven to 375°F.
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Heat 2 tablespoons of the olive oil in a medium skillet. Add the onion and garlic and saute until softened and translucent, but not brown. Season with 1/2 teaspoon salt and 1/4 teaspoon pepper. Stir in the thyme and basil. Spread the onion mixture into the bottom of a baking dish with a 6 cup capacity (like an 8-x-8-inch square).
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In a large bowl, toss the tomatoes and zucchini with 2 tablespoons of olive oil, 1 teaspoon salt, and 1/4 teaspoon pepper. Alternate the vegetables vegetables in compact upright rows on top of the onion mixture. Cover the dish with foil and bake until the vegetables have softened, about 30 minutes.
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In a small bowl, toss the panko with the remaining tablespoon of olive oil and nutritional yeast (or Parmesan), if using.
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Remove the foil from the vegetable dish and sprinkle with the panko mixture. Return to the oven and bake until the panko is toasted and golden-brown, about 20 minutes. Serve hot or at room temperature.