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Some indexes where added and seemed to help performance, though it is difficult to get an accurate metric because of the query caching used by the mysql server. I added an index to the hierarchy table on the name column, another index to the collectionobjects_common table on the objectnumber column, and two indexes to the relations_common table - one on the two columns ( documentid1, documenttype1 ) and another on the columns ( documentid2, documenttype2 ).
A persistent problem is the way some pre-installed vocabularies are implemented through the cspace-config file, since they do not accept or work properly with refnames.