How to prevent calls to System.exit() from terminating the JVM?

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Yes, this is possible using a SecurityManager. Try the following

class MySecurityManager extends SecurityManager {
  @Override public void checkExit(int status) {
    throw new SecurityException();
  }

  @Override public void checkPermission(Permission perm) {
      // Allow other activities by default
  }
}

In your class use the following calls:

myMethod() {
    //Before running the external Command
    MySecurityManager secManager = new MySecurityManager();
    System.setSecurityManager(secManager);

    try {
       invokeExternal();
    } catch (SecurityException e) {
       //Do something if the external code used System.exit()
    }
}

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