When the SageMath X.Y app is built, the sage root is /var/tmp/sage-X.Y-current. When the app runs it ensures that /var/tmp/sage-X.Y-current is a symlink to the sage root in the app bundle. Consequently, when building the sage_base the sage_base directory should be renamed as /var/tmp/sage-X.Y-current. The easiest way to arrange this is to use the build_base.sh script.
