Preheat oven to 400 degrees (200 degrees C). Heat 2 teaspoons ghee in a large skillet over medium-high. Gradually add spinach and cook until wilted. Remove to a paper towel-lined plate; set aside.
Wipe out the skillet and heat 3 tablespoons ghee over medium-high. Add onion and cook until very soft and translucent, 10 to 12 minutes. Add garlic and cook 5 minutes more. Add tomatoes and red-pepper flakes and cook until tomatoes have broken down and most of the liquid has been absorbed, about 15 minutes. Remove from heat; set aside.
Brush four 6-ounce (about 175-milliliter) shallow baking dishes with remaining 1 teaspoon ghee. Divide spinach equally among them, spreading evenly. Top with tomato mixture, creating a well in the center. Crack an egg into each well. Season egg with salt and pepper.
Place baking dishes on a baking sheet and transfer to the oven. Bake until the egg yolks are soft and egg whites are opaque, 15 to 18 minutes.
Serve topped with a pinch of black pepper and cilantro, if desired.
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