Manu shared with me what he wrote to his development team in order to clean WordPress. Here it is:
How to restore the WordPress installation to full health:
Do a manual full backup with the plugin BackupBuddy or a different system/plugin.
Use the plugin WP Maintenance Mode to enable the maintenance mode. This will serve a static page to everyone, except administrators.
Run the plugin WP Clean Up and delete all the drafts – Check if there is any draft that is not a RSS imported post (categorized as ‘imported-photo’).
DELETE orphan attachments with the following query: DELETE FROM [YOU_DATABASE_NAME].wp_posts WHERE post_type = ‘attachment’ AND post_parent NOT IN ( SELECT ID FROM ( SELECT ID FROM [YOU_DATABASE_NAME].wp_posts WHERE post_type <> ‘attachment’) as sub_query);