Add butter to skillet over medium heat. Once butter has melted, add onions, garlic, a good sprinkling of salt and pepper, and thyme. Allow onions to sweat down for about 10 minutes, then stir and let continue to sweat another 5 minutes.
Add wine and beef broth, simmering about 5-10 minutes or until wine starts to oxidize and turn brown. When onions are cooked through, drain and save the broth and wine mixture.
Add flour to wine and broth and boil mixture about 10 minutes it should be significantly reduced toabout 1/4 of what you started with.
Remove from heat and add cream.
Shape pizza dough into 10-12 inch diameter, 1/4 inch thick disk.
Put reduced sauce on dough.
Top with onions and then layer with chunks of Gruyere. Bake at 325 degrees on a middle to lower middle rack for about 15 minutes, checking to make sure the Gruyere doesn't burn.