Sift the flour into a large mixing bowl.
Add the salt, eggs, nutmeg and water and stir everything together thoroughly.
Cover the bowl with a tea towel and leave it for 20 minutes.
Prepare the onions by peeling them and chopping them width-ways into strips.
Heat the butter in a large frying pan or skillet set over a low-medium heat, and add the onions.
Sauté them for about 20 minutes, or until they’re soft and golden brown.
Preheat the oven to 140°C/275°F/Gas Mark 1.
Set a medium sized saucepan of water over a high heat and add a tablespoon of salt.
When the water begins to boil, set a Spätzle maker (or a colander) over the saucepan and drop some of the Knöpfle dough through it.
Once they’re in the pan, the Knöpfle only take about two minutes to cook.
Lift them from the water with a slotted spoon and drain them in a colander or sieve.
Pour the finished Knöpfle into a casserole dish and pop it in the oven to keep them warm.
When all the Knöpfle have been cooked and added to the casserole dish, add the cheese to the dish and mix everything together.
Return the dish to the oven for five minutes, or until the cheese has melted.
Pour the Käsknöpfle into individual serving bowls and top with the caramelized onion.
