Runtime rt = Runtime.getRuntime();
Process pr = rt.exec("java -jar map.jar time.rel test.txt debug");

http://docs.oracle.com/javase/7/docs/api/java/lang/Runtime.html

I found this in forums.oracle.com

Allows the reuse of a process to execute multiple commands in Windows: http://kr.forums.oracle.com/forums/thread.jspa?messageID=9250051

You need something like

   String[] command =
    {
        "cmd",
    };
    Process p = Runtime.getRuntime().exec(command);
    new Thread(new SyncPipe(p.getErrorStream(), System.err)).start();
    new Thread(new SyncPipe(p.getInputStream(), System.out)).start();
    PrintWriter stdin = new PrintWriter(p.getOutputStream());
    stdin.println("dir c:\\ /A /Q");
    // write any other commands you want here
    stdin.close();
    int returnCode = p.waitFor();
    System.out.println("Return code = " + returnCode);

SyncPipe Class:

class SyncPipe implements Runnable
{
public SyncPipe(InputStream istrm, OutputStream ostrm) {
      istrm_ = istrm;
      ostrm_ = ostrm;
  }
  public void run() {
      try
      {
          final byte[] buffer = new byte[1024];
          for (int length = 0; (length = istrm_.read(buffer)) != -1; )
          {
              ostrm_.write(buffer, 0, length);
          }
      }
      catch (Exception e)
      {
          e.printStackTrace();
      }
  }
  private final OutputStream ostrm_;
  private final InputStream istrm_;
}

One way to run a process from a different directory to the working directory of your Java program is to change directory and then run the process in the same command line. You can do this by getting cmd.exe to run a command line such as cd some_directory && some_program.

The following example changes to a different directory and runs dir from there. Admittedly, I could just dir that directory without needing to cd to it, but this is only an example:

Copyimport java.io.*;

public class CmdTest {
    public static void main(String[] args) throws Exception {
        ProcessBuilder builder = new ProcessBuilder(
            "cmd.exe", "/c", "cd \"C:\\Program Files\\Microsoft SQL Server\" && dir");
        builder.redirectErrorStream(true);
        Process p = builder.start();
        BufferedReader r = new BufferedReader(new InputStreamReader(p.getInputStream()));
        String line;
        while (true) {
            line = r.readLine();
            if (line == null) { break; }
            System.out.println(line);
        }
    }
}

Note also that I'm using a ProcessBuilder to run the command. Amongst other things, this allows me to redirect the process's standard error into its standard output, by calling redirectErrorStream(true). Doing so gives me only one stream to read from.

This gives me the following output on my machine:

C:\Users\Luke\StackOverflow>java CmdTest
 Volume in drive C is Windows7
 Volume Serial Number is D8F0-C934

 Directory of C:\Program Files\Microsoft SQL Server

29/07/2011  11:03    <DIR>          .
29/07/2011  11:03    <DIR>          ..
21/01/2011  20:37    <DIR>          100
21/01/2011  20:35    <DIR>          80
21/01/2011  20:35    <DIR>          90
21/01/2011  20:39    <DIR>          MSSQL10_50.SQLEXPRESS
               0 File(s)              0 bytes
               6 Dir(s)  209,496,424,448 bytes free

You are not capturing STDERR, so when errors occur you do not receive them from STDOUT (which you are capturing). Try:

CopyBufferedReader input = new BufferedReader(new InputStreamReader(
               pr.getErrorStream()));

First, the 'cd' command can't be executed by Runtime.exec() in the first place (see How to use "cd" command using Java runtime?). You should be able to just set the working directory for the process when you call exec (see below).

Second, running 'cmd.exe /c' to execute your process isn't what you want here. You won't be able to get the results of your process running, because that is returned to the command window -- which eats the error and then closes without passing the error along to you.

Your exec command should look more like this:

CopyProcess p = Runtime.getRuntime().exec(
    command, null, "C:\Users\Eric\Documents\COSC\ecj");

Where 'command' looks like this:

CopyString command = "java ec.Evolve -file ec\app\tutorial5\tutorial5.params"

Edit: For reading error messages, try this:

CopyString error = "";
try (InputStream is = proc.getErrorStream()) {
    error = IOUtils.toString(is, "UTF-8");
}
int exit = proc.waitFor();
if (exit != 0) {
    System.out.println(error);
} else {
    System.out.println("Success!");
}