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

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:

import 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

Here is the way to go:

Runtime rt = Runtime.getRuntime();
String[] commands = {"system.exe", "-get t"};
Process proc = rt.exec(commands);

BufferedReader stdInput = new BufferedReader(new 
     InputStreamReader(proc.getInputStream()));

BufferedReader stdError = new BufferedReader(new 
     InputStreamReader(proc.getErrorStream()));

// Read the output from the command
System.out.println("Here is the standard output of the command:\n");
String s = null;
while ((s = stdInput.readLine()) != null) {
    System.out.println(s);
}

// Read any errors from the attempted command
System.out.println("Here is the standard error of the command (if any):\n");
while ((s = stdError.readLine()) != null) {
    System.out.println(s);
}

Read the Javadoc for more details here. ProcessBuilder would be a good choice to use.

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:

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

Where 'command' looks like this:

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

Edit: For reading error messages, try this:

String 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!");
}