Metacat

-generate system meta for all docids, even those not originating on the server (replicas from the past)
-generate ORE docs and download remote data only for those documents that originated on this server being upgraded.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

refactor generate system meta loop to the factory class -- to be reused in sysmeta and ORE generation
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

do NOT generate ORE maps or download data when we do the initial System Metadata generation -- this is deferred until D1 registration.

make more generic so that a custom list of IDs can be passed in.

insert OR update system metadata -- no need to do an update right after initial insert...

call the System Metadata generator during upgrade to 2.0.0

In IdentifierManager.updateSystemMetadata(), add a check for invalid system metadata (fields that throw a NullPointerException on access) to ensure that system metadata is populated correctly. Updated calling classes to handle the exception.

only delete replicated data files (server_location != 1)

download remote data and save locally when it is referenced by an EML package, then include it in the ORE map.
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5522

upgrade routine to purge empty replicated data files so that they can be re-replicated
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5536