In a large skillet, pot, or Dutch oven, melt the butter over medium heat. Add the onions, and cook, stirring often, until deep golden brown, and caramelized - about 40 to 50 minutes. Stir in the garlic and thyme and cook, stirring often, for another minute.

Add the wine (if using) and stir until mostly evaporated, usually about 1 minute. Stir in the flour to coat the onions and cook, stirring often, for another 1 to 2 minutes.

Whisk in the beef stock and cream. Gently stir with a wooden spoon or spatula until slightly thickened, about 3 to 4 minutes. Stir in 1 tsp salt and ½ tsp black pepper. Remove from the heat.

Preheat oven to 375°F.

Grease your dish with softened butter or olive oil. Arrange a double layer of potatoes in the greased dish. Sprinkle salt and pepper over the potatoes. Spoon a thin layer of the sauce over the potatoes (you'll do about a quarter of the sauce). Sprinkle Parmesan cheese over the sauce. Repeat this process 3 to 4 more times (until you run out of potatoes, or sauce, whichever comes first).

Top the dish with the shredded Gruyère. Cover with foil and bake in the preheated oven (375°F) for 45 minutes. Remove the foil and bake for another 20 minutes, or until the cheese has browned in spots.

Remove the dish from the oven and let rest for 10 to 15 minutes. Or, cover with foil and let rest for up to 30 minutes. Garnish with chopped fresh herbs (ie, thyme), if desired. Serve immediately.