Of course, you have to extract all the files. The CleanProject utility does not work directly in the vault as well as BatchConverter, BatchProperties, DrawingTranslate, Integration, PowerPrint, SmartDrawings, UpdateVersion etc...
From the aforementioned tools, support now allows the integration of the connection to an EPDM vault. This integration is mainly located at the level of file selection (local copying, extraction from the vault, archiving) and evolves within each myCADtools tool for the functions of searching for use cases for example. These tools are accessible only with a myPDMtools license .