Heat ghee in a heavy-bottomed pot over medium heat. Add the sliced onions and fry them, stirring constantly, until they turn an even golden-brown. Watch them closely as they can burn quickly. Scoop them out immediately using a slotted spoon and spread them on a plate to cool and crisp up. Once cooled, crush them coarsely with your hands or pulse once in a blender (do not add water to make a paste).
In the same hot ghee remaining in the pot, add the green cardamom, black cardamom, cloves, and cinnamon stick. Let them sizzle for 30 seconds until they swell slightly and release a warm, spiced aroma into the air.
Add the mutton pieces to the pot. Increase the heat to medium-high and sear the meat for 5-7 minutes, turning occasionally, until the pinkness disappears and the surface turns a light brown. This locks in the juices.
Stir in the ginger-garlic paste and cook for 2 minutes until the raw smell fades. Reduce the heat to low, then add the Kashmiri red chili powder, coriander powder, and salt. Stir quickly to coat the meat, ensuring the dry spices do not burn.
Keep the heat on low. Pour in the whisked room-temperature yogurt slowly while stirring the pot continuously. Keep stirring for 2-3 minutes until the yogurt is fully integrated and starts to simmer gently. This constant motion prevents it from curdling.
Cover the pot with a tight-fitting lid, turn the heat to its lowest setting, and let the mutton cook in its own juices and the yogurt for about 45-50 minutes. Stir occasionally to ensure the bottom does not stick. The mutton is ready when it is tender and easily pierced with a fork.
Uncover the pot. Stir in the crushed caramelized onions, garam masala, and mace powder. Simmer uncovered for 5-8 minutes until the gravy thickens and a glossy layer of ghee separates on top. Turn off the heat and splash in the kewra water. Let it rest covered for 10 minutes before serving.