Melt the butter and olive oil in a large heavy pot over medium heat. Add the sliced onions, sugar, and a pinch of salt. Cook, stirring occasionally, until deeply golden and soft, about 25 minutes.

Stir in the garlic and thyme and cook for 1 minute. Pour in the wine, scraping up any browned bits, and simmer until nearly evaporated, about 2 minutes.

Add the beef broth, water, ½ teaspoon salt, and pepper. Bring to a boil, then add the pasta. Reduce the heat to a steady simmer and cook uncovered for 8 to 10 minutes, stirring often, until the pasta is tender and the liquid has reduced to a creamy sauce.

Remove the pot from the heat and stir in the grated Gruyère in two additions until fully melted. Taste for salt, spoon into bowls, and serve with extra thyme.