Adjust an oven rack to the middle position and heat the oven to 400 degrees. Lightly grease a 13 by 9-inch baking dish.

Heat the olive oil in a large nonstick skillet over medium-high heat until it shimmers. Add the onions and a pinch of salt; cook, stirring occasionally, until the onions are softened and deeply browned, about 15 to 20 minutes.

If the pan becomes too dark while cooking the onions, add the water and scrape up any browned bits with a wooden spoon. Once the water has evaporated and the onions are caramelized, stir in the garlic and cook until fragrant.

Remove the skillet from the heat and stir in the chopped olives. Season with a little pepper to taste.

Arrange half of the sliced potatoes in an even layer in the prepared baking dish. Season with salt and pepper, then sprinkle with half of the thyme. Spread half of the tomato slices over the potatoes, followed by half of the onion-olive mixture.

Repeat the layers with the remaining potatoes, more salt and pepper, the rest of the thyme, the remaining tomatoes, and the last of the onion mixture.

Bake uncovered until the potatoes are tender when pierced with a knife and the tomatoes have softened, about 45 to 60 minutes.

Sprinkle the Gruyère evenly over the top of the gratin. Return to the oven and bake until the cheese is melted, bubbling, and spotted with golden brown, about 10 to 15 minutes.

Let the gratin rest for 10 minutes before serving—this gives the juices time to settle so the slices hold their shape. Serve warm.