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