Preheat the oven to 325 degrees F.
Place the sauerkraut in a colander and rinse briefly to remove some of the salt from the brine: don't rinse it too much, or you will lose a lot of the flavor. (Alternately, if sauerkraut is not excessively salty, use as is.) Press to release most of the excess liquid and set aside.
In a large non-reactive skillet, melt 3 tablespoons of the butter over medium-low heat and add the bacon. Cook for 5 minutes, not allowing the bacon to brown. Add the onions and continue to cook until they are soft but not browned, about 8 to10 minutes. Transfer bacon-onion mixture to a 3 1/2 or 4 quart non-reactive ovenproof casserole or Dutch oven. Add the drained sauerkraut and toss to combine. Using a small piece of cheesecloth, make a bouquet garni with the thyme, bay leaves, peppercorns, juniper berries, and garlic and place in the baking dish. Add the ham hocks, chicken stock, and beer and stir to combine. Cover the pot and bake for 2 hours, undisturbed.
While the sauerkraut is baking, melt the remaining tablespoon of butter in a large skillet over high heat and brown the sausages on both sides. Set aside.
When the sauerkraut and hocks have baked for 2 hours and the hocks are tender, remove the casserole from the oven. Place the potatoes on top of the sauerkraut. If the liquid has evaporated to below 2/3 full level, add a bit more water to the casserole at this time. Cover the casserole and return it to the oven. Cook for about 30 minutes, or until the potatoes are tender.
Remove the casserole from the oven again and place the browned sausages on top of the sauerkraut mixture, cover, and return to the oven until the sausages are heated through and the potatoes are tender, about 15 more minutes. Remove the bouquet garni and serve immediately, with each person receiving some of each of the sausages, part of a hock, potatoes and sauerkraut. Pass the mustard at the table as a condiment.
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