Place onions in a sauté pan with the olive oil and caramelize, about 45 minutes to an hour. Add a bit of water as needed until the onions are soft, browned, and sweet. Add the garlic, thyme, and vinegar and cook until the vinegar reduces and sweetens.
Boil the pasta for about 3 minutes, then strain.
Add the cream and salt to the onions, then the beef stock and remove from heat.
Mix the cheeses together in a large bowl and set aside.
Add panko to medium bowl, then about ⅓ of the cheeses.
Add the onion mixture to the large bowl with the ⅔ of the cheese, then add the strained pasta and mix well.
Pour the onion and pasta mixture into a 9x13" pan, and top with the panko/cheese mixture and bake at 375 F for about 15 to 20 minutes until the breadcrumbs are browned.
Note:
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