Building on @Tim's example to make a self-contained method:
import java.io.BufferedReader;
import java.io.File;
import java.io.InputStreamReader;
import java.util.ArrayList;
public class Shell {
    /** Returns null if it failed for some reason.
     */
    public static ArrayList<String> command(final String cmdline,
    final String directory) {
        try {
            Process process = 
                new ProcessBuilder(new String[] {"bash", "-c", cmdline})
                    .redirectErrorStream(true)
                    .directory(new File(directory))
                    .start();
            ArrayList<String> output = new ArrayList<String>();
            BufferedReader br = new BufferedReader(
                new InputStreamReader(process.getInputStream()));
            String line = null;
            while ( (line = br.readLine()) != null )
                output.add(line);
            //There should really be a timeout here.
            if (0 != process.waitFor())
                return null;
            return output;
        } catch (Exception e) {
            //Warning: doing this is no good in high quality applications.
            //Instead, present appropriate error messages to the user.
            //But it's perfectly fine for prototyping.
            return null;
        }
    }
    public static void main(String[] args) {
        test("which bash");
        test("find . -type f -printf '%T@\\\\t%p\\\\n' "
            + "| sort -n | cut -f 2- | "
            + "sed -e 's/ /\\\\\\\\ /g' | xargs ls -halt");
    }
    static void test(String cmdline) {
        ArrayList<String> output = command(cmdline, ".");
        if (null == output)
            System.out.println("\n\n\t\tCOMMAND FAILED: " + cmdline);
        else
            for (String line : output)
                System.out.println(line);
    }
}
(The test example is a command that lists all files in a directory and its subdirectories, recursively, in chronological order.)
By the way, if somebody can tell me why I need four and eight backslashes there, instead of two and four, I can learn something. There is one more level of unescaping happening than what I am counting.
Edit: Just tried this same code on Linux, and there it turns out that I need half as many backslashes in the test command! (That is: the expected number of two and four.) Now it's no longer just weird, it's a portability problem.