In a large bowl, mix the flour, eggs, water, salt, and nutmeg until a thick batter forms. The consistency should be somewhat stretchy but still thick enough to hold.

Bring a large pot of salted water to a rolling boil. This will be used to cook the spätzle.

Using a spätzle maker or a colander, press the dough through the holes into the boiling water. Cook until the noodles float to the surface, which takes about 2-3 minutes. Remove with a slotted spoon.

In a large skillet, melt the butter over medium heat and add the sliced onions. Sauté until they are golden brown and caramelized, about 10-15 minutes.

In a large mixing bowl, layer the cooked spätzle with the sautéed onions and shredded cheese. Toss gently to combine.

Transfer the mixture to a buttered baking dish. If desired, sprinkle extra cheese on top and bake in a preheated oven at 350°F (175°C) for about 20 minutes until the cheese is bubbly and golden.

Serve hot, garnished with fresh herbs if desired.