Preheat the oven to 400 degrees. Prepare a 3.5 qt braiser with butter or cooking spray. Cut the potatoes in ⅛ inch slices using a sharp knife or mandoline. Arrange the potato slices in circles, slightly overlapping, in the bottom of the braiser, and add ¼ teaspoon salt to each layer before beginning the next layer.

In a medium sized skillet, add the olive oil and truffle oil on medium heat. Add the onions and 1 teaspoon salt, and cook until golden brown and caramelized, about 20-30 minutes. Add chicken broth to deglaze the pan, then add the heavy cream, thyme bunch, and bay leaves. Bring the mixture to a simmer and cook until slightly thickened, about 5-6 minutes. Remove the thyme and bay leaves and stir in 1 cup Gruyere cheese, stirring until smooth and melted. Remove the mixture from the heat and let cool slightly. Stir in the creme fraiche and season with salt and pepper.

Pour the cream mixture over the potatoes and sprinkle the remaining ½ cup Gruyere cheese on top. Season with salt and pepper and arrange the caramelized onions evenly on top. Bake until golden brown on top and is tender in the middle when pierced with a knife, about 45 minutes to an hour. Allow the gratin to cool for about 15 minutes before serving. Garnish with thyme leaves, chives and flaky sea salt and drizzle with additional truffle oil for extra flavor.