Preheat a large, deep skillet with a tight fitting lid over medium-high heat. Add olive oil. When shimmering, add onions and garlic, season generously with salt and pepper, and cook, stirring occasionally, until onion is softened and just beginning to turn golden on the edges, about 12 minutes. Do not brown.
Push onions to the edges of skillet and add one tablespoon olive oil to the center. Add harissa paste to olive oil. Saute until fragrant and caramelized, about 3 minutes, stirring to incorporate the onion and garlic mixture. Add tomatoes and simmer until reduced and slightly thickened, about 15 minutes. Season to taste with salt and pepper.
Reduce heat to low. Gently crack eggs into tomato sauce, forming a small well with a spoon for each egg to land. Season tops of eggs with salt and pepper, cover skillet, and cook until eggs are just set, about 5 minutes.
Remove from heat (eggs will continue to cook in the sauce), and top with feta, cilantro, and a final drizzle of olive oil. Serve immediately, with toasted rustic bread on the side.