I don't believe I am particularly interested in setting JAVA_HOME by
default. After all, given a choice of N different JVMs a user may have
installed, which one should be chosen?

Additionally, Debian policy (unsure about Ubuntu's) does not allow a
program to require a certain environmental variable to be set to run
properly. Knowing that then, which program is it you are running that
does not function without JAVA_HOME?

update-alternatives is also not very useful in the current Java
situation (this will change with OpenJDK). At this point there are some
applications which require certain JVMs to be able to function.
Basically, a per-app compatibility list. The /etc/jvm.d mechanism seeks
to address this.

Hopefully, when we have one completely functional standard JDK, this
won't be an issue though.

-- 
update-java-alternatives does not change the JAVA_HOME
https://launchpad.net/bugs/45348

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