Mix the flour and salt in a bowl, create a well in the middle. Whisk together the milky water and eggs, gradually pour into the well while stirring, mix everything together and beat until the dough starts to bubble. Cover and leave to stand at room temperature for approx. 30 mins.
Gradually press the dough through a spaetzle sieve into simmering salted water. As soon as the spaetzle rise to the surface, remove them with a slotted spoon, drain and keep warm.
Mix the onions and garlic with the flour, sage and fennel seeds. Heat the clarified butter in a non-stick frying pan. Fry the onions for approx. 20 mins. over a medium heat until crispy, stirring occasionally. Remove, season with salt and set aside.
Gently fry the bacon in the same pan until crispy, without adding any oil. Remove from the pan and drain on paper towels. Wipe away the cooking fat. Add the spaetzle, cheese and water to the same pan, heat through until the cheese melts, stirring occasionally. Season. Crumble the bacon, serve the bacon and fried onions on top of the spaetzle.