For the application server, for additional security, you should restrict access to the file system.
In general, only the owner should have full access to create or update files on the system.
Also, for the Provisioning Service, the file upload directory is by default the temp directory for your system. The directory is configured using the upload-file-directory variable in plan.xml. You should change this setting to be a directory appropriate for your installation, and set the directory permissions to only allow the owner to have read and write access.