Cut whole chicken into pieces and trim excess fat and remove skin if preferred. Take one lime and cut in half. Clean each chicken pieces by rubbing lime halves while squeezing some of the juice out. Repeat process for each chicken pieces. Rinse chicken well with water and pat dry. Add chicken to a large bowl and set aside. In a small bowl, mix juice of 1 lime (approximately 2 tablespoon), chicken bouillon, scallions, vinegar, parsley, thyme, cloves, garlic, pinch of salt, and black pepper. Add spice mixture and make sure all pieces are well coated. Cover and refrigerate for at least 2 hours or overnight.
Remove bowl from refrigerator and bring to room temperature. In a heavy skillet, heat 2 tablespoon oil with 1/2 tablespoon of tomato paste under medium heat while stirring to mix. Remove chicken from marinade and slowly add to hot oil. Do not crowd the pan. Brown chicken on all sides in batches. Transfer to a plate.
Heat remaining oil in skillet add marinade to cook for 1 minute. Add chicken to pan and stir to incorporate. Add remaining tomato paste into 1 cup of boiling water to dilute and add to chicken. Cook covered over medium heat until chicken is fully cooked. Remove from heat, remove chicken from pan and strain liquid to remove extra spices residue. Reheat sauce in same pan, add 1/4 water (or more if necessary), season with additional salt and pepper and hot pepper or hot sauce if preferred. Add onion slices and bell pepper if using, and bring to a boil. Once sauce starts to thickens, add chicken and cook uncovered for 5 to 7 minutes on medium to low heat. Remove from heat and serve immediately.