I used the following hack at the end of my main method to get around the problem:
if (Boolean.parseBoolean(System.getenv("RUNNING_IN_ECLIPSE"))) {
System.out.println("You're using Eclipse; click in this console and " +
"press ENTER to call System.exit() and run the shutdown routine.");
try {
System.in.read();
} catch (IOException e) {
e.printStackTrace();
}
System.exit(0);
}