Season short ribs on both sides with salt and black pepper. Heat oil in a heavy-bottomed skillet over medium-high heat. Cook short ribs in batches, turning a few times, until browned on all sides, about 10 minutes per batch. Remove short ribs to a large lidded plastic tub while you make the marinade.
Pour 1 1/2 cups water, cider vinegar, and red wine vinegar into the warm skillet and bring to a simmer. Cook and stir, scraping any browned bits off the bottom on the pan. Add juniper berries, cloves, and bay leaves, season with salt and black pepper. Remove from heat and pour in 1 cup cold water. Pour mixture over the ribs and place in an ice bath until chilled, 30 to 40 minutes. Cover and marinate in the refrigerator for 24 hours.
Melt butter in a large,heavy pot or Dutch oven over medium heat. Cook and stir onion, celery, and carrot in the melted butter until the vegetables are softened, about 10 minutes. Add garlic and cook for 1 minute. Place marinated short ribs over the top of the onion mixture. Pour in remaining marinade from the plastic tub and stir in 1 cup water, chicken broth, and sugar.
Bring to a simmer over medium-high heat. Reduce heat and simmer on low, covered, until meat is fork-tender, 3 to 4 hours. Remove meat to a platter. Discard juniper berries, cloves, and bay leaves. Sprinkle cooked onion mixture over the top of the meat, reserving excess cooking liquid in the pan.
Place pot with remaining cooking liquid over medium-high heat. Grind gingersnaps in a food processor until fine and to the liquid in the pan. Stir in balsamic vinegar and boil until reduced and thickened, skimming fat, about 20 minutes. Season with salt to taste. Strain gravy through a fine mesh sieve, spoon over the beef, and serve.
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