I decided to update my owncloud instance to version 7 and came across a problem where the database update errored out due to an issue with primary key conflicts in the ocu_lucene_status. lucene is the full text search engine by apache. I was able to get around it by truncating the table and redoing the update.
Owncloud updated ok after that, and everything appears to be working apart from apps, which I had to clear my browser cache to get to appear. This is apparently a known issue. There appears to be something else going on as well, as not all the apps are appearing in the list. This might be an unrelated problem, as there are other people with the same issue.
