Heat oil in a heavy based pan on medium heat. Add onions and fry (stirring occasionally) until golden brown. Add tomatoes and saute until they are well soft.
Add in the chicken pieces, plain yogurt , ginger paste, garlic paste, salt, red chilli powder and turmeric powder. Mix and cover pot and let it cook on low heat until the chicken is half done.
Seperately put a frying pan on stove on medium heat and roast the mustard seeds, cumin seeds, fennel seeds and nigella seeds in a dry pan. (Do not use oil.) Roast these seeds until the cumin turns brown.
Take 2 teaspoons of this roasted mixture and set it aside. Grind the rest of it in a grinder to a fine powder. Then add the turmeric powder to this grinded powder and make it into a thick paste by adding the lemon juice. Now stuff this paste into the green chillies and set them aside.
Add the remaining paste to the chicken and sprinkle the roasted mixture over the chicken and further cook the chicken until it is well done. Then add the stuffed chillies to the chicken and cook on very low heat for another 5 minutes.