Directories created by Rational Rhapsody could be either the project directory (for example, MyProject_rpy) or directories created to contain packages.
The *_rpy directory becomes a VOB element once you connect to the archive.
In addition, package directories can be made into VOB elements when you initially create them (for more information, see the property definitions of ConfigurationManagement::ClearCase::MakeCMShadowDirActivation and ConfigurationManagement::ClearCase::MakeCMShadowDir on the Properties tab of the Features window in Rational Rhapsody).
However, in the situation where you try to "add to source control" for a Rational Rhapsody element and the operation fails because the parent directory is not a VOB element, you can make the directory a VOB element using IBM Rational ClearCase®, then continue working in Rational Rhapsody.