The documentation mentions using the *.conf / *.conf.bat files to make their customizations.  It would be good to have a 'Note' around these areas in the documentation that makes it clear that users should not modify the startup scripts like standalone.sh/domain.sh/etc as there can be bugs in these scripts which get fixed via an Update which would cause the user a conflict.  So the users should just modify the .conf files otherwise they would have to overwrite their changes and apply the Update and then reapply their changes.