When removing projects and documents in WebCenter, their files and database entries are not removed immediately (for speed reasons). Instead, they are marked for deletion in the database so you don't see them anymore in the user interface. To remove these files from the filestore, you must regularly (typically every night) run the cleanup script, called Cleanup.bat.
This removes all restfiles from deleted projects and removes entries which are no longer used in the database.
However the following error can occur:
"Could not log into WebCenter properly. Make sure to submit correct authentication credentials."
For WebCenter 12.1 and newer, this error should not appear anymore.
WebCenter 12.0 and before:
There is the access.properties file in the config folder that contains the credentials of the user used by the cleanup tool to login to WebCenter. By default, they are the (encrypted) credentials of the ADMIN user. So, you have to make sure the password in this file is the same one as the encrypted password of the ADMIN user. You can find it in the Pwrd column of the Users table in the WebCenter database.
Edit the access.properties file in the config folder (typically at C:\Esko\Artios\WebCenter\ApplicationServer\Cleanup\config folder) for the Cleanup.bat file.
Change the password field to the password of the Admin user that you can find in the Pwrd column of the Users table in the WebCenter database (this is an encrypted version of the admin password).
Try running the cleanup script again (you need not restart any service).