In a Dutch oven or a large, deep, heavy-bottomed pot, combine tomatoes, apples, onions, brown sugar, granulated sugar, vinegar, garlic, chipotle pepper, salt and cloves. Bring to a boil over high heat, stirring often.

Reduce heat and boil gently, stirring often and reducing heat further as mixture thickens, for 45 minutes. Stir in raisins. Cook, stirring often, for 15 to 20 minutes or until thickened. Test for doneness.

Ladle into sterilized jars to within 1/2 inch (1 cm) of rim. Remove any air pockets and adjust headspace, if necessary, by adding chutney. Wipe rims. Apply prepared lids and rings. Tighten rings just until fingertip-tight.

Process jars in a boiling water canner for 10 minutes. Transfer jars to a towel-lined surface and let rest at room temperature until cooled. Check seals.