Deleted files in archive cause NPEs which in turn cause misleading errors

This affected snipr and needs to be resolved.

When a file is deleted in the archive but the entry remains in the catalog XML, the catalog utils try to get the file and assumes it succeeded. This causes an NPE that can get misinterpreted by code above it.

This should check that the file for each entry exists. If so fine, if not log an error indicating that the catalog contains a misleading entry then proceed.

The root cause of the deleted files is unknown and that just shouldn't happen, but XNAT needs to handle the case as it happens.