1. Preheat oven to 400 degrees. Spread tomatoes in a single layer on 2 rimmed baking sheets. Drizzle each sheet with 1 tablespoon oil; sprinkle each with 1/2 teaspoon thyme, and season with salt and pepper. Bake until tomatoes have softened, about 20 minutes. (Leave oven on.)

2. Process bread in a food processor until coarse crumbs form. Melt 1 tablespoon butter with remaining tablespoon oil in amedium skillet over medium heat. Add breadcrumbs, and toss to coat. Season with salt and pepper; set aside.

3. Bring a large pot of water to a boil over high heat. Add 1 tablespoon salt and the pasta. Cook pasta until almost al dente, about 5 minutes. Drain, and run under cold water to stop cooking. Transfer to a large bowl; set aside.

4. Whisk 1/2 cup stock into the flour in a medium bowl; set aside. Melt remaining tablespoon butter in a medium saucepan over medium heat. Stir in nutmeg, cayenne, remaining 1/2 teaspoon thyme, and 1 teaspoon salt. Add milk and remaining 1 1/2 cups stock. Whisk in flour mixture. Bring to a boil, whisking frequently. Reduce to a simmer. Cook 8 minutes, whisking frequently. Add cheeses; cook, stirring, until melted. Pour over macaroni, stirring to combine.

5. Put eight 4 1/2-by-1 1/4-inch ramekins on a baking sheet. Put 2 tomato slices in bottom of each ramekin. Divide macaroni mixture evenly among ramekins. Top each with a tomato slice. Sprinkle with breadcrumbs and thyme sprigs. Bake until bubbling and golden brown, about 30 minutes. Serve immediately.