Add butter to a large skillet over medium low heat. When melted, add onions and stir until well coated in butter.
When onions are turning transparent, after about 10 minutes of cooking, stir in brown sugar and apple cider vinegar.
Continue cooking for 30-40 minutes, stirring every 5 minutes or so, until onions are well caramelized. Stir in salt and pepper.
Pre-heat oven to 500 degrees and place pizza pan or stone in oven.
Roll pizza dough out into a 12-inch circle on a lightly floured surface.
Remove pan or stone from oven and place dough on top. Lightly brush with olive oil.
Sprinkle mozzarella cheese over the dough. Top with caramelized onions and chopped thyme. Layer shaved or grated gruyere cheese over the top.
Bake pizza at 500 degrees for about 9-11 minutes, until dough is nice and crispy.
Remove from oven and sprinkle chopped parsley over the top.