ISABELLE_JDK_HOME settings variable points to JDK with javac and jar (not just JRE);
update for prospective jdk1.7.x component;
#!/usr/bin/env bash
#
# Author: Makarius
#
# Augment Java extension directories.
## diagnostics
function fail()
{
echo "$1" >&2
exit 2
}
[ -n "$ISABELLE_HOME" ] || fail "Missing Isabelle settings environment"
## main
exec "$ISABELLE_JDK_HOME/bin/java" \
-classpath "$(jvmpath "$ISABELLE_HOME/src/Tools/JVM/java_ext_dirs.jar")" \
isabelle.Java_Ext_Dirs "$(jvmpath "$ISABELLE_HOME/lib/classes/ext")"