Preheat oven to 400°F. Season chicken with salt and pepper. Place in a small skillet and add cold water to cover. Bring to a simmer over medium-high heat. Reduce heat to medium-low and cook, turning once or twice, until opaque and firm, about 10 minutes. Remove, let cool and cut into small pieces or shred. You should have about 3 cups cut-up chicken.
Spread one-third of sauce over bottom of a 7-by-11-inch baking dish. Arrange 3 tortillas, slightly overlapping, on top. Sprinkle one-third of chicken and cilantro over tortillas. Top with a third of cheese. Make two more layers of sauce, tortillas, chicken, cilantro and cheese. Arrange tomato on final layer of cheese. Cover with foil and bake until bubbly, about 20 minutes. Remove foil and cook until top is lightly browned, 10 minutes more.
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