refs.c: make prune_ref use a transaction to delete the ref

refs.c: make prune_ref use a transaction to delete the ref

Change prune_ref to delete the ref using a ref transaction. To do this we also
need to add a new flag REF_ISPRUNING that will tell the transaction that we
do not want to delete this ref from the packed refs. This flag is private to
refs.c and not exposed to external callers.

Signed-off-by: Ronnie Sahlberg <sahlberg@google.com>
Reviewed-by: Michael Haggerty <mhagger@alum.mit.edu>
Signed-off-by: Jonathan Nieder <jrnieder@gmail.com>