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:
name=JPackage (free), generic
exclude=ant, ant-antlr, ant-apache-bcel, ant-apache-log4j,
ant-apache-oro, ant-apache-regexp, ant-apache-resolver,
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.