do not write keys imported from file into git

Without this MR, any job loading encoding keys from a manifest file which are not in git will attempt to copy those keys into git. This MR distinguishes the keys cached in the (python) registry which are created from scratch (and thus have to be preserved, either by writing to git or to the manifest file) from those which are imported from a manifest file (which are thus known, and thus are already preserved, and do not necessarily have to be archived, by the reading job, into git).