Convert item attributes, refererences and collections to simple objects.

Signed-off-by: Richard Smith <rnsmith100@gmail.com>
Test fix.
tidy up config
Changes to address the concerns raised in #712
Handle config correctly. Refs #810
variable scope is important! Refs #810
all identifier sources only ever store SO terms, so use more specific key. Refs #832
Prevent precomputed table being generated when web service table request is made. Fixes #712.
Merge pull request #785 from rnsmith/beta

Log a warning message instead of SQL ERROR if precomputed table index cr...
address some ontology term merging issues. Refs #832
checkstyle fix
key fix Refs #832
for LOOKUP queries with wildcards, return when there is a match. Refs #676
Close bobo results, but still not clearing MemoryManager thread.
Set flag to attempt to delete Timer threads left open undeployed webapps, doesn't seem to be working.
Added enrichment identifiers to download function.
raise batch size
Merge pull request #808 from rnsmith/simple-items

Item attributes, references and referencelists are simple objects
checktyle Refs #808
merge beta into branch