In ST 5.4 we do not have a maintenance application to clean up transferred files from user account subscription folders.
In ST 5.5. we have a new maintenance application called "File Maintenance". It allows you to specify exactly what files to delete older than x days.
More details here: https://docs.axway.com/bundle/SecureTransport_55_AdministratorGuide_allOS_en_HTML5/page/Content/AdministratorsGuide/applications/applicationsFileMaintenance.htm
https://support.axway.com/en/articles/article-details/id/153003/do/search