When starting JIRA (v6.3.9), I get this message on stderr:

Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=384m; support was removed in 8.0

I think this is because the ${PRGDIR}/bin/permgen.sh program doesn't actually test if MaxPermSize is valid, it only tests if the java runtime environment is IBM-branded. This is weird because the java program used is the JRE that was offered by Atlassian: /opt/atlassian/jira/jre/bin/java

java version "1.8.0_11"
Java(TM) SE Runtime Environment (build 1.8.0_11-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.11-b03, mixed mode)

It's a minor problem, but could get worse over time. I monkeypatched my own version to detect 'IBM' or 'version "1.8' but that will break when the next JRE from Atlassian is Java 9 (version 1.9.x)