Thanks Nate!
I’ve upgraded to 3.3.0.4, which seems mostly to have worked, however I now can’t access the Administration page in the dashboard – I get a 404. The menu link doesn’t include the journal path, so it looks like mydomain.org/index/admin instead of mydomain.org/journal/index/admin or mydomain.org/index.php/index/admin (which loads when entered manually, except CSS and JSON calls mostly fail).
Is there a change to htaccess that should be made for such an upgrade path? I searched the docs but can’t find anything about it.