CloverETL supports versioning systems in general (such as SVN, CVS, Git etc). This is simply because ordinary CloverETL projects are stored as files on the disk. You can version them as any file - either by tools in Eclipse or by external tool such as TortoiseSVN. We don't ship a specific versioning system with CloverETL, you need to install one of your choice into the Designer - for example Subclipse for SVN.
The situation is a bit more complex when developing Server graphs - the versioning systems don't directly support files that are stored remotely in a sandbox. In such case you need to maintain a local copy of the sandbox project, that can be versioned as usual.