Prepare the cipollines, onions, and shallots:

Trim, peel and slice thinly. To peel the cipolline onions easily, trim the root end and drop in boiling water for 2 minutes, then transfer to an ice bath to stop the cooking. Spread the cipollines out on a towel to dry. The skin should slip off quite easily at this point.  To make slicing more stable, cut the cipollines in half from root to stem and lay cut side down on a cutting board. Slice cross-wise into half rings.

Divide butter between two heavy-bottom stockpots (or one stockpot and one large skillet).  Likewise, divide both kinds of onions and the shallots between the pans, and sauté until deeply golden brown, about 20 – 25 minutes.

Deglaze the pans:

Divide the port between pans, and reduce until almost evaporated, scraping up brown bits.  Transfer all onions to one stockpot.

Simmer:

Add tomatoes and simmer 5 minutes.

Puree 2 cups of the onion-tomato mixture with 2 cups beef stock and add puree back to stockpot. Alternatively, add 2 cups beef stock to the pot and pulse with an immersion blender a couple times to thicken the mixture, while leaving lots of texture in tact. Add remaining beef stock, thyme and salt and pepper.  Bring to a boil, reduce heat and simmer for 1 hour. Taste and adjust seasonings.

Prepare garnish:

Fold each prosciutto slice in half and arrange on a foil-lined sheet pan. Sprinkle with Gruyere and about half the Parmesan. Melt the cheese until bubbly and the prosciutto starts to crisp under the broiler. 

Serve:

Divide the soup between bowls and float a prosciutto on each bowl.  Sprinkle lightly with remaining Parmesan and top with chopped parsley.