Combine tomatoes, onions, apple cider vinegar, salt, cloves, ginger, and cinnamon in a large stock pot over medium heat. Bring to a boil, reduce heat to low, and simmer until tomatoes have broken down and liquid has reduced by 1/3, about 2 hours. Stir apples into the relish and simmer, stirring occasionally, until apple pieces have started to break down but are still small pieces, about 30 more minutes.
Sterilize jars, lids, and rings in boiling water for at least 5 minutes. Pack the tomato relish into the hot, sterilized jars, filling the jars to within 1/4 inch of the top. Run a knife or a thin spatula around the insides of the jars after they have been filled to remove any air bubbles. Wipe the rims of the jars with a moist paper towel to remove any food residue. Top with lids, and screw on rings.
Place a rack in the bottom of a large stockpot and fill halfway with water. Bring to a boil and lower jars into the boiling water using a holder. Leave a 2-inch space between the jars.
Pour in more boiling water if necessary to bring the water level to at least 1 inch above the tops of the jars. Bring the water to a rolling boil, cover the pot, and process for 15 minutes.
Remove the jars from the stockpot and place onto a cloth-covered or wood surface, several inches apart, until cool. Once cool, press the top of each lid with a finger, ensuring that the seal is tight (lid does not move up or down at all). Store in a cool, dark area.
