What does "No Groovy Runtime found. Rule-Execution will be disabled" mean?
The Rule-Engine will be configured with groovy-scripts. Therefore the groovy-runtime is required which cannot be distributed from the Eclipse.org servers as long as the groovy runtime is not approved by the Eclipse IP team. If you want to track the status of that issue please add yourself as cc at CQ 4417. To install a groovy execution environment open the Eclipse Marketplace, switch to the Remus marketplace and search for 'groovy'. After the installation of the groovy bundle this message should disappear.
Does the automatic synchronization overwrite my local data?
Short answer: Yes and no. If you're synchronizing information units with a remote repository, the automatic synchronization leaves all local modified elements and remote deleted elements. That means the automatic synchronization updates only local unmodified information units and adds new remote information units locally.
The easiest way of sharing your data in Remus is to use the Local Folder or Webdav connector. With this connector you can point to a folder on your local disk or on a shared network-folder and Remus synchronizes all the data in with this folder. For an example how to share data see the screenscast