1. Begin the Rye Sour Starter: Combine the rye flour, yeast, warm water, crushed caraway seeds and minced onion in a large bowl and stir with a wooden spoon until smooth. The mixture should have a thin, soupy consistency. Cover with plastic wrap and allow to stand in a warm spot until bubbly and fermented. It can be left for up to 24 hours.
2. Prepare Stage One: In a large bowl, combine the water, 1¼ cups of the flour, and the starter; stir with a wooden spoon until smooth. The dough should pull slightly and may start to come away from the sides of the bowl. Wipe down the sides of the bowl and sprinkle the remaining ¼ cup flour over the entire surface of the sour. Cover with plastic wrap and let stand until doubled in size and the floured top appears cracked with openings spread widely apart. This could take 4 to 8 hours (avoid letting the mixture collapse).
3. Prepare Stage Two: To the Stage One sour, add the water and ¾ cup of the flour; mix until smooth. Wipe down the sides of the bowl and sprinkle the remaining ¼ cup flour over the entire surface of the sour. Allow to rise in a warm area for 4 to 8 hours, or until doubled in size.
4. Prepare Stage Three: To the Stage Two sour, add the water and the 1 cup flour. Mix until smooth. Add more flour, ¼ cup at at time, until a dough-like consistency is reached. Cover with plastic wrap and leave in a warm spot until doubled in size, 4 to 8 hours. At this point, the starter is ready to be used in the bread.
The caraway seeds can be ground in a coffee or spice grinder or with a mortar and pestle.
When preparing Stages One and Two, the object is to make a thick consistency as close as possible to that of a soft dough. If the mixture is too soupy, add more flour ¼ cup at a time and mix until smooth.
It is recommended that Stage One and Two be made on the same day, the second stage refrigerated overnight, and the third stage prepared the morning of baking. If you intend on baking the bread first thing in the morning, then prepare the third stage the evening before, so it can rise slowly all night and be ready in the morning.
The sour starter can be refrigerated; it is recommended that it be stirred down every 3 to 4 days if it hasn't been used. Every 10 to 12 days, dispose of half of the starter and refresh it by mixing in equal amounts of rye flour and water. If there is some discoloration on top, it can be skimmed off.