Apps in templates?

So the message from Microsoft is that sandbox solutions are "deprecated" in SharePoint 2013 and that we should build apps - which I have, however when the users try to save site templates they get:

Sorry, this site can't be saved as a template. It contains apps that don't work in templates:

<Your App Name Here>

So my question is, are there any circumstances where Apps are allowed in Web Templates? (i.e. does anyone know if this message can be avoided) and if not, has anyone thought of a way to get a custom webpart into a web template that can be used on-prem and cloud?

Thanks,

   James.

James Boman - http://www.boman.biz Software Consultant for IPMO - http://www.ipmo.com.au