Preheat the oven to 375°F (190°C) and lightly grease a small baking dish or 8-inch oven-safe skillet.

Melt the butter with the olive oil in a large skillet over medium-low heat.

Add the sliced onions and a small pinch of salt.

Cook for 25–35 minutes, stirring occasionally, until the onions are soft and deeply golden. Reduce the heat if they begin burning.

If browned bits stick aggressively to the pan, add 1–2 tablespoons water and scrape them into the onions.

Add the diced apple and cook for 4–6 minutes, until slightly tender but still holding its shape.

Add the garlic and cook for approximately 30 seconds.

Stir in the fresh thyme and apple cider vinegar.

Remove approximately 1/2 cup of the caramelized apple and onion mixture and reserve for topping.

In a large bowl, combine the softened cream cheese, sour cream, Dijon mustard, and black pepper.

Reserve approximately 1/2 cup of the combined shredded cheddar and Gruyère.

Fold the remaining shredded cheese into the cream cheese mixture.

Fold in the caramelized apple and onion mixture remaining in the skillet.

Taste and add salt only if necessary.

Transfer the mixture to the prepared baking dish.

Sprinkle the reserved shredded cheese over the surface.

Spoon approximately half of the reserved apple-onion mixture over the cheese.

Bake uncovered for 18–22 minutes, until hot and gently bubbling around the edges.

If desired, broil very briefly for additional browning, watching constantly.

Remove from the oven and add the remaining caramelized apples and onions.

Garnish with a few fresh thyme leaves.

Rest for approximately 5 minutes.

Serve warm with toasted baguette, crackers, pretzel crisps, or fresh apple wedges.