In a small skillet over medium-high heat, saute onion in butter until tender. Stir in ham and tomato; set aside.
In a small bowl, combine biscuit mix and water. Press onto the bottom and 1/2 in. up the sides of a greased 13x9-in. baking dish. Spread ham mixture over the crust; sprinkle with cheese. In a bowl, beat the eggs, milk, dill, salt and pepper; pour over cheese. Sprinkle with chives.
Bake, uncovered, at 350° for 25-30 minutes or until a knife inserted in the center comes out clean. Let stand for 5 minutes before cutting.