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

When managing obsoletes/obsoletedBy system metadata fields, set the archived flag to false initially, and set it to true on system metadata for objects that a revision obsoletes.

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.

check that the resourceMap (based on Id only) does not currently exist in the local metacat when generating OREs

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.

Properly initialize the servlet context when starting alternate servlets, which makes sure that the configuration files have been loaded and config properties are available.