maintain classpath in more elementary manner: turn ISABELLE_CLASSPATH into -classpath option, so that all jars are covered by sun.misc.Launcher.AppClassLoader (e.g. relevant for loading add-on resources);
ignore $ISABELLE_JAVA_EXT -- do not change java.ext.dirs;
#!/usr/bin/env bash
#
# Author: Makarius
#
# DESCRIPTION: invoke Java within the Isabelle environment
declare -a JAVA_ARGS; eval "JAVA_ARGS=($ISABELLE_JAVA_SYSTEM_OPTIONS)"
isabelle_jdk java "${JAVA_ARGS[@]}" \
-classpath "$(jvmpath "$ISABELLE_CLASSPATH")" "$@"