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With the use of the drush command 'hosting-import', we are capable of 'refreshing' the frontend system with changes that may have been directly applied from the command line using Provision.
Examples of this include verifying/building a platform, installing and migrating sites. hosting-import magically 'discovers' these changes and syncs the frontend in to match.
I have noticed that after running provision-delete on a site, even though we retain an alias for the site in ~/.drush (by design or bug?), running hosting-import doesn't mark the site as deleted in the frontend.
This appears to be because there's nothing in the backend that really identifies the site as having been deleted: it's simply gone, other than the alias.
If we are going to keep the alias around (if not, we should be running drush @foobar provision-save --delete in a post_delete hook in my opinion, but that can be a separate ticket..), then we should be changing the 'site_enabled' status to 'false' or something more specific like 'deleted', that might be able to communicate this change to the frontend.
Setting site_enabled to 'false' and running hosting-import probably isn't ideal, it might be considered 'disabled' (I haven't actually tried this yet though).