Make the filling: Heat oil in a large skillet and add chopped onions. Sauté 5 minutes over med heat. Add chicken, tomatoes, garlic, spices and water. Simmer for a few more minutes until most of the liquid is gone.
Place cheese in middle of tortilla and then top with about 1/2 cup of chicken mixture. Fold edges and then roll up. Place seam side down in a lightly greased baking dish.
Brush each chimichanga with melted butter. Place in a preheated 400 degree oven and bake for 20 minutes or until lightly browned.
Prepare sauce. While chimichangas are baking, in a small saucepan heat stock. Mix flour and half and half until well blended. Stir into stock and simmer until thickened. Stir in chilies, lemon and lime juice and salt and pepper. Top chimichangas with sauce when serving and add avocado slices and chopped tomatoes as garnish.