Preheat oven to 350 degrees. Butter a baking dish (or a piece of foil laid over a baking dish for easy clean up).
Cut a thin slice off the stem end of the tomato and scoop out the seeds and pulp. Sprinkle liberally with salt and pepper and turn upside down on some paper towels to drain for about 10 minutes. Break egg into tomato shell, sprinkle with a bit more salt and pepper and bake for about 20-25 minutes or until egg is just set. Combine the cheese with the chives and sprinkle on top of the egg. Return to oven for a minute or two until the cheese has melted.
This would be fabulous with some crispy bacon and a nice thick piece of toasted gluten-free bread.