applying (-a) (for verification).

generated deltas.

exists, it will come up with a unique name.  usage_apply() in
aux.pm updated to reflect this.

Changed method name from list_stable_dbIDs to list_stable_ids for consistency with the rest of the API. Also minor POD changes.

Minor POD reformatting.

Added more systematically-named list_dbIDs and list_stable_dbIDs to replace list_geneIds and list_stable_geneIds; the old functions are still there for backwards compatibilty but now print a warning and call the appropriate list_ function. Common functionality for list_ functions is in BaseAdaptor.pm.

Conserver space by keeping at most two databases locally.  Might
still not be good enough to create deltas for mart.