Heat olive oil in a large high-sided ovenproof skillet or short-sided pot over medium-high heat. Add thinly sliced onions, a pinch of kosher salt, and a pinch of freshly ground black pepper and cook, stirring occasionally and adding 1 Tbsp. water and scraping bottom of the pan if starting to burn, until onions are a deep mahogany color and jammy, 30–35 minutes
Add garlic and thyme and cook, stirring often, until fragrant, about 1 minute. Add white wine and cook, stirring occasionally, until reduced by about half, about 3 minutes
Add 5.5 cups water and bring to a simmer. Add pasta and cook, stirring often to prevent pasta from sticking to bottom of pan, until almost all of the liquid has been absorbed, a thick sauce has formed, and pasta is al dente, 10–14 minutes
Remove pot from heat and add parmesan, butter, mustard, sugar, Worcestershire sauce, salt to taste, and pepper to taste. Stir until cheese is melted
Place a rack in upper third of oven; heat broiler. Scatter gruyere over pasta and broil until melted and golden brown in spots, 2–5 minutes depending on your broiler
Serve with chives as garnish