Wash and soak rice and lentils in water for at least 15 minutes, then drain for at least 15 minutes.
In a large non-stick pot, heat oil and 3 tbsp ghee and sauté onions until golden. Add whole spices (bay leaf, cardamom, cinnamon sticks, whole black peppers, and cumin seeds) and sauté for another minute.
Add garlic paste, ginger paste, salt, turmeric, red chili powder, and coriander. Add a splash of water to prevent burning. Sauté for about 5 minutes here.
Add the drained rice and lentils and toast them in the masala for 5-7 minutes, continuously stirring on medium heat. Keep scraping the bottom of the pan to prevent sticking.
Add hot water (have this boiling on the side while you're working on the other steps). Mix well, taste the water for salt, and adjust accordingly.
Let it come to a boil on high heat, uncovered (should be about 6-7 minutes). The amount of water at this point should be level with the rice.
Cover, lower the heat, and cook for about 15 minutes until the rice and lentils have softened and all the water has been fully absorbed. Do not stir vigorously at this point, as this will cause your khichuri to become too mushy. You can gently insert your spoon to the bottom of the pot to check if all the water has been absorbed. Add green chilies and the remaining 1 tbsp ghee.