You have to remember that there are a number of theme developers who have not implemented a (visible) versioning system in their themes. If Waterfall were to overwrite these themes as they are, then you can expect pandamonium to break-out from users who have suddenly lost months of theme modifications! Editing of themes is something that has always been possible and tools like RWMultiTool and RW Theme Miner have allowed you to enter themes to change things like images for your own.
With this in mind, Jonathan at Nimblehost had a frighteningly complex task on his hands when designing and building Waterfall. Kudos to him. The system he arrived at makes an automated backup of every theme (when an update is downloaded), to remove the liability and risk associated with theme updates wiping modifications. It does the same for all themes - the system cannot handle updates differently for different themes.
What I am trying to explain is that yes, Waterfall will remove the theme from your /themes/ folder and put it into /Waterfall/backups. But you can very easily go to this folder (via the manage addons option in the RW menu), select the theme, put its extension back to .rwtheme and put it back into your themes folder again. The theme NEVER EVER leaves your RapidWeaver addons folder. Nothing is deleted or overwritten. If you still need the original theme (like to access custom images), you can still go back to it again at any time.
Also from what I gather, quite a few people use Waterfall purely for getting notification about updates. They may choose to manually go to the developers website, read what has changed in the latest version, and download the theme using their existing link. And again, the new theme wonât override the older version if versioning is setup and supported by that particular theme company.
As Iâve mentioned lots and lots of times in my support documentation, duplication and renaming of themes is recommended by most (not all) theme developers. I am certainly one who advocates it. Duplication means the theme becomes yours to do what you want with. Should you need technical support of customisation made, then it so much easier for all involved to be working off a duplicate. Duplicates are omitted from Waterfall update checking. RW6 adds a special âtheme was duplicatedâ string to the theme.plist file, to differentiate it from regular âoff the shelfâ themes.