Metacat

MOdified MetacatHandler to catch cases where ObjectFormat is not being set properly on data files when
generating SystemMetadata. When the EML document contains a format for an entity that maps to a null
type in ObjectFormat.convert(), then the type ends up being null and an error is generated on insertion...

allow "docid override" queries to include the results of a "normal" query - if the operator is left null, it acts as the usual override, otherwise UNION and INTERSECT modes can be used to either augment or refine the results.
this is for incorporating semantic+spatial+keyword queries into one query operation/result

remove System.out statements in favor of logging

Removed hardcoded D1 node type in ResourceHandler and added in a new 'dataone.nodeType' property. Also added 'dataone.coordinatingNodeBaseURL' property which points to the CN that stores the authoritative object format list. If this instance of Metacat is a CN, it may point to itself.

ResourceHandler in Metacat was set to return the KNB site URL as the MN base URL rather than the node Id. Fixed. https://redmine.dataone.org/issues/1390

initialize the HandlerPluginManager

allow the addition of properties via code

add event notification for insert/update/delete on documents (for semtools plugin)

do not attempt to check permissions when reading documents for systemMetadata generation (unless I completely do not understand this feature - please verify!).

do each table separately with it's own connection - running into memory issues on dev.nceas running this.