Melt butter in a large skillet over medium heat. Add onions, 1/2 tsp salt, and 1/4 tsp black pepper and cook, stirring, until wilted. Cover, and continue to cook, stirring every few minutes, until onions are very soft and pale golden, about 20 minutes. Remove from heat and cool completely.

Working with one crust at a time, on a lightly-floured work surface, roll to a thickness of 1/8 inch. Using a 2 1/2 inch round cutter, cut as many disks as possible. Lightly roll each disk thinner into a 3-inch circle. Press into mini-muffin pan. You can re-roll scraps once or twice.

When all the crusts are rolled, place crusts in freezer for at least 30 minutes.

Preheat oven to 350°F.

In a large bowl, whisk together crème fraîche, eggs and yolks, nutmeg, thyme, remaining 1/2 tsp salt, and remaining 1/2 tsp black pepper. Stir in the onions.

Remove crusts from freezer and fill with about 1 tablespoon of filling each. Top with grated cheese.

Bake until crusts are golden, filling is puffed and set, about 25 minutes. Let cool in the pan for 15-30 minutes.

Serve either warm or room temperature.