In Sitefinity, themes and master pages are kept in a website template. You can check the website template file structure in the documentation
. Sitefinity Thunder creates the website templates based on this structure.
If you upload a website template to your web site through Sitefinity Explorer, the theme and master page will be automatically registered. If you create the website template locally, you will need to create a page template based on the master page manually because a page template needs to be created in the database. The theme should still be registered automatically but there is an issue that has been introduced with Thunder's latest version. This will be fixed for the next update. Until we release this fix, you could register the theme manually
I am sorry for any inconvenience that this might have caused you.
the Telerik team
Do you want to have your say in the Sitefinity development roadmap? Do you want to know when a feature you requested is added or when a bug fixed? Explore the Telerik Public Issue Tracking
system and vote to affect the priority of the items