lib: Fix endless upgrade problem

48db8c8 introduced a disagreement between when
notmuch_database_needs_upgrade returned TRUE and when
notmuch_database_upgrade actually performed an upgrade.  As a result,
if a database had a version less than 3, but no new features were
required, notmuch new would call notmuch_database_upgrade to perform
an upgrade, but notmuch_database_upgrade would return immediately
without updating the database version.  Hence, the next notmuch new
would do the same, and so on.

Fix this by ensuring that the upgrade-required logic is identical
between the two.