Tomato Soup with Roasted Peppers, Garlic and Onions With Gruyere Grilled Cheese Croutons

2 onions, peeled and sliced into thin wedges EVOO, for liberal drizzling 2 tablespoons fresh thyme leaves Salt and freshly ground black pepper 2 heads garlic, ends trimmed to expose cloves 2 large sweet red peppers 2 cups chicken stock One 28- to 32-ounce can fire roasted tomatoes 2 cups passata or tomato sauce 1 1/2 teaspoons dried herbes de Provence, half a palmful A few leaves fresh basil, torn