public class scriptListener implements IPatternMatchListenerDelegate {
  ...
  public void matchFound(PatternMatchEvent event) {
    ...
    PlatformUI.getWorkbench().getDisplay().syncExec(new Runnable() {
        public void run() {
            ...
            process = Runtime.getRuntime().exec("myscript "+arguments);
            BufferedReader in = new BufferedReader(new InputStreamReader(process.getInputStream()));
            BufferedReader err = new BufferedReader(new InputStreamReader(process.getErrorStream()));
            process.waitFor();
            while((line = in.readLine()) != null)
                output+=(line+"\n");
            ...etc...

public class scriptListener implements IPatternMatchListenerDelegate {
  ...
  public void matchFound(PatternMatchEvent event) {
    ...
    PlatformUI.getWorkbench().getDisplay().syncExec(new Runnable() {
        public void run() {
            ...
            // This closes all old consoles.
            ConsolePlugin.getDefault().getConsoleManager().removeConsoles(
                 ConsolePlugin.getDefault().getConsoleManager().getConsoles()
            );
        
            // Create a new console for the script result.
            outConsole = new MessageConsole("myscript results", null);
            ConsolePlugin.getDefault().getConsoleManager().addConsoles(new IConsole[] { outConsole } );
        
            // Create a stream to the console and print the scripts output there.
            MessageConsoleStream consoleStream = outConsole.newMessageStream();
            
            // Start the external script and set up streams to read its output.
            process = Runtime.getRuntime().exec("myscript "+arguments);
            BufferedReader in = new BufferedReader(new InputStreamReader(process.getInputStream()));
            BufferedReader err = new BufferedReader(new InputStreamReader(process.getErrorStream()));

            boolean break_on_next = false;
                  boolean ready = false;
                  for (waitIndex = 0; waitIndex < (pluginMaxWaitTimeInSeconds*10); waitIndex++) {
                
                    // Read the input stream, i.e. ordinary output from the script.
                    ready = in.ready();          // Check if the next read operation 
                                                 // is guaranteed not to block for input.
                    while (ready == true) {      // Keep reading as long as the stream
                                                 // is ready for a new read.                        
                        line = in.readLine();    // Read one line of output.
                        if (line != null) {
                            consoleStream.println(line);
                            consoleStream.flush();
                            ready = in.ready();    // Check if the stream is 
                                                   // ready for a new read.
                        }
                        else
                            ready = false;
                    }
                    
                    // Read the error stream, i.e. error messages from the script.            
                    ready = err.ready();
                    while (ready == true) {            // For comments about this code,
                                                       // see similar code above.                    
                        line = err.readLine();
                        if (line != null) {
                            consoleStream.println(line);
                            consoleStream.flush();
                            ready = err.ready();
                        }
                        else
                            ready = false;
                    }
                    
                    try {
                        // This code is a bit special since we want to do
                        // the last read from the scripts streams
                        // _after_ the script for sure has finished. 
                        // If the script has ended, then the for-loop
                        // above should end on the next loop.
                        if (break_on_next == true)
                            break;
                        
                        process.exitValue();      // The return value is ignored.
                        break_on_next = true;     // When this line is reached there was
                                                  // no exception from exitValue(), i.e. 
                                                  // the process is finished. Break the for-loop
                                                  // after next readLine.
                        
                    } catch (IllegalThreadStateException e) {
                        // This exception means that the subprocess represented by this Process object 
                        // has not yet terminated. So the for-loop above should run again.                    
                        try {
                            Thread.sleep(100);    // Wait a while for the script to execute (milliseconds).
                        } catch (InterruptedException ie) {
              }
                    }
                } // End of for-loop            
        
            } catch (IOException e1) {
                consoleStream.print( "Plugin error!" );
            }
        ...