Cut the top off of each tomato and scoop out the pulp. Reserve both the lid and the pulp. Sprinkle with salt and turn upside down on paper towels to drain. Melt butter in medium sized saucepan and saute first onion until transparent about 7 minutes. add garlic, the tomato pulp, tomato paste and thyme. Simmer, covered, over low heat for 35 minutes. Season with salt and pepper. Add sugar and then puree mixture in blender. Sprinkle with first tablespoon of parsley. Preheat oven to 350 degrees. Let the bread soak in the milk for 10 minutes. Melt butter in small skillet and saute onion until soft. Squeeze bread dry and discard milk. In large bowl, combine sauteed onion, bread, meat, garlic, egg and parsley. Season with salt and pepper. Sprinkle with nutmeg. Butter a glass baking dish. Fill tomatoes with meat mixture and place lids on top. Bake for 35 minutes. Reheat tomato sauce and serve over each tomato.