In a 12-inch to 14-inch sauté pan, heat olive oil until smoking. Add onion and garlic and cook until soft but not browned, 5 to 6 minutes. Add chili flakes and eggplant and cook, stirring regularly until softened and lightly browned, about 8 to 10 minutes. Add tomatoes, basil and thyme and bring to a boil. Simmer 15 minutes and season to taste with salt and pepper.