My simple solution to this problem has been to add an exclude= line to
my jpackage.repo file listing the names of all the Java packages that
shipped with FC4:
[jpackage-generic]
name=JPackage (free), generic
mirrorlist=
http://www.jpackage.org/jpackage_generic.txt
failovermethod=priority
gpgcheck=1
gpgkey=
http://www.jpackage.org/jpackage.asc
enabled=1
exclude=ant, ant-antlr, ant-apache-bcel, ant-apache-log4j,
ant-apache-oro, ant-apache-regexp, ant-apache-resolver,
ant-commons-logging, ...
and so on. The list of packages was built by grepping for
[0-9]*jpp_[0-9]*fc from the list of the packages that shipped with FC4,
then stripping off the version numbers.
When I first saw the problem mentioned on this list I was surprised
that the
jpackage.org site didn't suggest something like this to
prevent JPackage packages from replacing the Fedora ones.
-Mark.