Grate the zest off the lime and mix with the ginger, thyme, and minced garlic. Mix with the olive oil. Rinse the chicken and pat dry. Loosen the skin around the breast and legs with your fingers. Rub the herb mixture under the skin. Cut the lime in half and put into the chicken cavity. Prepare the baking dish. Slice onions about a half-inch thick. Cover the bottom of a baking dish with one layer of onions. Center the chicken breast-side up on the bed of onions. Cut tomatoes in half lengthwise. Scoop out seeds and discard. Place skin-side up around the chicken. Sprinkle peeled garlic cloves around the chicken. Preheat oven to 450 degrees. Roast the chicken for 45 minutes. Remove from oven and test the leg-thigh joint with an instant-read thermometer. It should read 165 to 170 degrees. Let the chicken rest for 15 minutes to allow juices to settle into meat. Remove skin, carve, and serve with vegetables and skimmed pan juices.