Fixes WFE-1257. Commonly used namespaces are put as prefixes. Turtle
output uses the RO URI as base.
Fixes WFE-1179. Add RDF file extensions to annotation bodies with no
name provided.
Don't fail if the RO bundle doesn't exist.
Fixes WFE-1256. Update Jena to 2.11.0 and TDB to 1.0.0.
Only set prefixes if the transaction has just started.
Make sure saving prefixes always works.
Bring back ontology cache'ing. Refs WFE-1217.