I think that the jira upgrade script logic is failty because it will break installs by replacing files which should not be raplaced, like:
bin/setenv.sh -- place to put JVM config, you have to modify it for real production env (medium-big instances)
conf/server.xml -- also you need to modify it to allow jira to accept a frontend webserver
bin/jirabanner.txt --- you need to empty it in order not to spam your console with FancyARTs 
... from all services I've seen on linux Jira is the only one that is spamming restart script
jre/lib/security/cacerts -- if you installed any certificates for connecting to other services SMTP/IMAP/LDAP/..., you will loose them on upgrade
Do you agree this this? Do you have any other thigs to add to the list?
