The timeout implemented in RunCommand.java does not trigger a proper error escalation. I still don't get an exitcode after a timeout in the onvoking process. My java skills are slightly rusty - so correct me if I'm wrong, but from your code (lines 203-209) I understand you're using java.util.concurrent.ExecutorService.shutdown() which causes an orderly shutdown and after that in line 209 you return 'returnCode[0]' which I suppose is initialized to literally zero as well. Therefore an invoking process does not get notified, that an irregular termination (due to a timeout) occurred, which makes error handling cumbersome. IMHO a timeout should push an error/exception up the call-stack.

...and here's a suggestion, how this issue might get resolved. Take it with a grain of salt, as I'm not a Java expert though...
I think the solution is using the return Value of the awaitTermination Method to determine the returnValue of your own function, like ...

if (!executorService.awaitTermination(timeoutInMinutes, TimeUnit.MINUTES)) {
        returnCode[0] = 1; // or whatever exitcode you might assign a timeout - except zero!
}

According to the API doc awaitTermination() returns true if this executor terminated and false if the timeout elapsed before termination.