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Step 1
In a large bowl, beat together the eggs, milk, salt, pepper, and nutmeg. Gently stir in the flour, a little at a time, until just combined. Do not overmix. If too thick, add a little more milk. If too thin, add a little more flour. Let sit for 20 minutes.
Step 2
In a large cast iron or nonstick skillet, melt 1 tablespoon of the butter over medium-low heat. Add the onions and cook, stirring occasionally, until golden brown and caramelized. Remove to a plate.
Step 3
While the onions are caramelizing, bring a large pot of water to a simmer. Place a spaetzle press or large-holed colander over the pot and fill with batter. Slide the press back and forth or use a wooden spoon to press the batter through the holes of the colander to create the dumplings. Cook until the dumplings float to the top. Remove with a strainer and drain well.
Step 4
Place the skillet over medium heat and melt the remaining tablespoon of butter. Once thoroughly heated, add the cooked dumplings and toss with the cheese until melted. Leave the pan undisturbed for a couple of minutes to create a golden brown crust along the bottom and sides of the dumplings.
Step 5
Remove from heat and serve hot topped with the caramelized onions and chives.