When retrieving the last of the goodies from meat dishes, the skeletal bones are cooked (stewed) in water w/ seasonings. Most recipes have all sorts of vegetables included. but what if the desire is a beef, lamb, pork, or chicken base to be stored and used at a later time. Regardless, the "stock" resulting is usually "skimmed" of excess fats or grease.

What additions are initially appropriate (seasonings &/or vegetables) before the stewing and skimming that such ingredients will not be congealed and removed w/ the fat?

We used to throw in Egg shells to help clarify the stock, then filter later.
Don't know how much goes out with the fat?

carrots, onions, celery (Base of all stocks) either ends and scraps or just rough cut and added to stock (skins and all)

tomato scraps or ends or just chopped up tomato is added for beef stocks