Heat butter and olive oil in large heavy-bottomed pot over medium heat until butter is melted and foaming.

Add sliced onions, salt, and pepper. Cook, stirring occasionally, for 25-30 minutes until deeply caramelized and golden brown.

Reduce heat to medium-low if browning too quickly. Focus on slow, even caramelization for maximum flavor development.

Add garlic and fresh thyme to caramelized onions. Cook 1-2 minutes until fragrant, careful not to burn garlic.

Pour in white wine to deglaze, scraping up browned bits. Let wine reduce by half, about 3-4 minutes.

Add beef broth, water, bay leaf, dried thyme, and nutmeg. Bring to rolling boil over high heat.

Add pasta to boiling liquid, stirring well to prevent sticking. Cook according to package directions minus 2 minutes, stirring frequently.

Test pasta for almost al dente doneness. Liquid should be mostly absorbed but still saucy.

Remove from heat and discard bay leaf. Stir in 1 cup Gruyere and all Parmesan until melted and creamy.

Let rest 2-3 minutes for flavors to meld and sauce to thicken. Adjust seasoning with salt and pepper.

Serve immediately in warmed bowls, topped with remaining Gruyere, parsley, and thyme. Accompany with crusty bread.