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Preheat oven to 375° F.
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Cut tomatoes in half horizontally across the middle of the tomatoes (cut crosswise). Grate, with the cut side of the tomatoes down on a box cutter. Discard tomato skins and reserve juices and pulp in box grater (see photo above).
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In a small skillet heat oil over medium-high heat. Add onion and season with salt and pepper. Cook for 5-7 minutes until onion has soften and is starting to brown. Add garlic and cook, stirring for 2-3 minutes. Add red wine (if using) and deglaze the skillet. Cook allowing wine to completely reduce. Add tomato juices, pulp and thyme sprigs, and bring to a boil. Reduce heat to medium and cook until most of the tomato juices has evaporated., about 7-10 minutes. Remove from heat and set aside.
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With a mandolin or a very sharp knife, cut zucchini, eggplant and pepper into 1/4" thick slices.
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In a small oven-proof dish place tomato mixture on the bottom. Top in a circular repetitive patter with zucchini, eggplant, and pepper slices.
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Cook in oven for 40-50 minutes until vegetables have softened, but aren't brown.