How to Make It
Preheat the oven to 350°. In a large pot of boiling salted water, cook the potato-and-cheese pierogi until they are just done, about 3 minutes. Drain and gently shake off any excess water. Arrange the pierogi in a 3-quart baking dish in an even layer.
In a large skillet, cook the sliced bacon and kielbasa over moderately high heat, stirring occasionally, until they are lightly browned, about 5 minutes. Using a slotted spoon, transfer the bacon and kielbasa slices to a plate.
Melt the butter in the skillet. Add the onion and cook over moderate heat, stirring occasionally, until softened, about 6 minutes. Add a few tablespoons of water if the onion seems very dry. Add the sauerkraut and juniper berries, season with salt and pepper and cook, stirring, for 2 minutes. Add the flour and cook for 1 minute, stirring. Add the stock and bring to a boil. Stir in the bacon and kielbasa and spoon the mixture over the pierogi. Cover with foil and bake for 30 minutes, until heated through. Uncover and bake for 10 minutes longer. Let stand for 10 minutes before serving.
In a small bowl, mix the sour cream with the whole-grain mustard. Serve with the pierogi choucroute.