Metacat

log error when looking up non-existent local SM rather than completely bombing out of the resynch thread.

look up docid using mapped guid when checking permission on described data file
Addresses: http://support.nceas.ucsb.edu/rt/Ticket/Display.html?id=7490

use docid (not guid) when instantiating the PermissionController. Was getting an error with DOI-ified identifier and the metacat getaccesscontrol action:
https://knb.ecoinformatics.org/knb/metacat?action=getaccesscontrol&docid=Collinge.3.28
<error>
AccessControlForSingleFile.getACL() - MCDB error when getting ACL: No guid registered for docid doi:10.5063/AA/Collinge.3.28...

make sure we have non-null values where jibx serialization expects them for LogEntry

use secure Metacat context URL for D1 registration
https://redmine.dataone.org/issues/3030

first pass: DataONE-specific log retrieval to avoid java-based post-processing.

set archived flag (true) when we set the obsoletedBy value in the ORE system metadata

use the localId for obsoletes/obsoletedBy ORE system metadata (https://redmine.dataone.org/issues/2964)

Print the stack trace when the MMP cannot be resolved.

report errors during XML->HTML transform
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5618