Upgrade tut_upgrade "Auxillary features" section if implemented.

I've done this, but a bit differently.

The integrity checker now always 'quarantines' rather than deletes - which means moving stuff under _old/.
I think that's better: no need to have multiple options and a complex UI to manage them all.

It doesn't touch themes. But you can easily use keep_theme=default in the URL to force the default theme.