Combine all ingredients in a pan, cover, and cook over very low heat for 1 to 1-1/2 hours, until the chiles are very soft and the liquid has reduced down to 1 cup. This recipe will keep for several weeks in the refrigerator in an airtight container. For chipotle puree, place cooked chipotles and sauce in a blender, and puree. Put through a fine sieve to remove seeds.