Heat ghee in a large heavy-bottomed pot or Dutch oven over medium heat.
Add the thinly sliced onions and fry until they turn dark golden brown, about 15 minutes.
Stir in the ginger garlic paste and cook for one minute until fragrant.
Add the beef shanks and sauté for 5 to 7 minutes until the meat is browned on all sides.
Stir in the Nihari masala powder and Kashmiri red chili powder. Cook for an additional 2 minutes, adding a splash of water to prevent burning.
Pour in 5 cups of water and bring the stew to a boil. Reduce the heat to low, cover tightly, and simmer for 4 to 6 hours, or until the beef is incredibly tender.
In a small bowl, whisk the whole wheat flour with 1 cup of cold water to create a smooth, lump-free slurry.
Gradually pour the flour slurry into the simmering stew while stirring continuously to prevent lumps from forming.
Simmer the stew on low heat for another 15 to 20 minutes until the gravy thickens and the oil naturally rises to the top.
Garnish with julienned ginger, fresh cilantro, sliced green chilies, and a squeeze of fresh lemon wedges.
Serve hot with warm naan bread.