1. To make the sauce, warm 1 tablespoon of olive oil in a skillet over medium heat. Add the onion and cook, stirring frequently, until they’re soft and wilted, 2 to 4 minutes.
2. Reduce the heat to low and add the garlic and salt, stirring for a minute or so, until the garlic softens. Stir in the red pepper flakes, cumin, and za’atar, stirring for about 30 seconds to release their fragrance.
3. Add the tomatoes and any juice in the can. Increase the heat to medium, and cook for 5 to 6 minutes, stirring frequently, until the mixture is thick and still juicy, but not runny. Turn off the heat and add the cilantro. Set aside. (The sauce can be refrigerated for up to five days in advance.)
4. To make the bread, whisk together the flour, salt, and yeast in a medium bowl. Stir in the water using a rubber spatula until the dough becomes a sticky ball. Cover the bowl with a damp kitchen towel or plastic wrap until doubled in size, 1 1/2 to 2 hours.
5. To assemble the shakshukas, line two baking sheets with parchment paper or silicone baking mats. Put 3 individual teaspoons of olive oil in three puddles, equally spaced apart, on each baking sheet. Sprinkle 1/2 teaspoon of sesame seeds over each pool of olive oil.
6. Using two forks, scrape the dough from the edges of the bowl toward the center, to deflate it, then use the forks to shape the dough into a rough ball.
7. With the two forks, working from the center, separate the dough into two equal portions. Use a pastry scraper or spatula to transfer half of the dough onto a lightly floured countertop. Cut the dough into three equal pieces and roll each into a smooth ball, pinching the bottom seam closed as you tighten it up and roll it closed.
8. Place each round of dough on top of the puddle of olive oil and sesame seeds and roll it around to coat it. Let the dough rest for 20 minutes.
9. Preheat the oven to 350ºF (180ºC).
10. Using lightly oiled hands, stretch the balls of dough into disks, until the dough starts pulling back and resisting. Let the dough relax for 5 minutes, then stretch each one into a 6 or 7-inch (16cm) round.
11. Divide the shakshuka sauce in the centers of each round of dough and spread it almost to the edges with the back of a soup spoon, leaving a 1/2-inch (2cm) border. Use the spoon to make a crater-like deep impression in the center of each round of dough and sauce, which will hold the egg later. Brush the exposed rims with water and sprinkle with some additional sesame seeds.
12. Bake the shakshuka bases for 15 minutes, rotating the baking sheets in the oven, and switching them on racks, midway during baking.
13. Remove the breads from the oven and use a soup spoon to redefine and deepen the indentation in the center of the sauce, and create little rims in the sauce, so the egg won’t run out. Crack an egg into the center of each. (Tip: You might find it easier to crack each egg into a small bowl or teacup first, then tilt them into the breads.)
(As you place the egg on top of each, use a tablespoon to futz with the sauce and build a fortress-like barrier, if some of the egg wants to run out.
14. Carefully put the baking sheets back in the oven and bake, rotating the baking sheets as they cook, until the whites of the eggs are just cooked and the yolks are barely set, 8 to 12 minutes. Serve warm.