Layered Spring Omelet

Name: Layered Spring Omelet
Ingredients: 1 tablespoon olive oil; 8 ripe tomatoes, seeded and cut into 1/2-inch dice; 3/4 teaspoon coarse salt, plus more to taste; 1/2 teaspoon freshly ground pepper, plus more to taste; 21 large eggs; 1/2 teaspoon ground nutmeg; 1/2 teaspoon cayenne pepper; 3 tablespoons unsalted butter; 3/4 cup grated Vermont cheddar cheese; 3/4 cup grated Gruyere cheese; 2/3 cup loosely packed fresh basil leaves, torn in half; 8 ounces spinach, leaves picked and torn in half; 1 tablespoon chopped fresh thyme leaves; 1 small leek, julienned, for garnish; 2 tablespoons snipped fresh chives, for garnish