Heat the olive oil in a medium ovenproof skillet over medium-high heat. Add the onion and bell pepper and cook, stirring occasionally, until tender, about 10 minutes. Add the cilantro stems, garlic, cumin, paprika and red pepper flakes; season with 1/4 teaspoon salt and a few grinds of pepper. Cook, stirring, until the garlic is softened and the vegetables are coated with the spices, about 1 minute.
Preheat the oven to 375 degrees F. Stir the tomatoes with their juices into the skillet. Reduce the heat to maintain a low simmer and cook, stirring occasionally, until the tomatoes break down and the sauce thickens slightly, about 20 minutes; season with salt and pepper.
Use the back of a spoon to make 4 wells in the sauce, 1 to 2 inches apart. Crack an egg into each well. Run the edge of a rubber spatula through the egg whites to break them slightly, being careful not to break the yolks (this allows the egg whites to cook faster). Transfer the skillet to the oven and bake until the egg whites are just set, 15 to 18 minutes. Season with salt and pepper and top with the cilantro leaves. Serve with pita bread.
Photograph by Ryan Dausch