Preheat the oven to 300 degrees F.
Warm the oil in a large skillet over medium-high heat for 3 minutes. Meanwhile, season the ribs well with salt and pepper on both sides. Put eight ribs into the skillet. Sear for 2 minutes per side, or until a golden crust has formed. Transfer to a roasting pan and repeat with the remaining ribs.
Add the celery, carrots, and garlic to the skillet and cook, shaking occasionally, until the veggies are lightly brown, 3 to 5 minutes. Remove the veggies drain off the excess oil, leaving about 2 tablespoons in the skillet, and return to the heat. Put the veggies back in the skillet, along with the tomatoes, juniper berries, peppercorns, broth, and 1 cup of the wine. Bring the mixture to a boil then carefully pour it over the ribs. Cover the roasting pan and place it in the oven for 3 hours.
Remove the pan from the oven and place the ribs on a serving platter. Set aside until cool enough to handle. Strain the braising liquid into a saucepan, skim as much of the grease from the top as possible, and discard the solids. Place the saucepan over high heat, add the remaining cup of wine and tomato paste and bring to a boil. Reduce the heat to medium and reduce the liquid to 2 cups. Make a paste of the butter and flour and add to the sauce 1 tablespoon at a time until the sauce is slightly thickened.
Once the ribs are cool enough to handle, remove the meat from the bone (it should slide right off). Pull the meat and set aside.
Toss the squash with olive oil, season with salt and pepper and place on a baking sheet. Roast until slightly dark and soft. Remove to a shallow pan and set aside.
Pour the flour into a large bowl and add the parsley, nutmeg, salt and pepper. Mix the eggs with the water and melted butter and pour into the flour mix. Stir well to combine. Add the cheese and stir again. Boil a big pot of salted water and push the batter through the holes of a colander in batches. Boil until cooked through, about 4 minutes. Drain and toss with a little oil to prevent sticking.
When ready to serve, add 3 cups spaetzle to a skillet. Add 1 ½ cups of sauce, the tomatoes, squash and shallots. Cook until warmed through. Divide into 4 Pyrex dishes or soup plates and top with 5 ounces of short rib meat. Garnish with flat leaf parsley and serve.