Apparently, update.php tried to create the changes table / indexes even if they already exist, which causes a fatal error.
Creating wb_changes table ...A database query syntax error has occurred.
The last attempted database query was:
"CREATE INDEX wb_changes_change_type ON wb_changes (change_type)
"
from within function "DatabaseBase::sourceFile( /var/www/daniel/wikidata/extensions/Wikibase/repo/sql/changes.sql )".
Database returned error "1061: Duplicate key name 'wb_changes_change_type' (localhost)"
Version: unspecified
Severity: normal