To use it with ProcessBuilder you must separate the commands like this:

final List<String> commands = new ArrayList<String>();                

commands.add("cmd.exe");
commands.add("/C");
commands.add("start");
ProcessBuilder pb = new ProcessBuilder(commands);
pb.start();

The java.lang.ProcessBuilder and java.lang.Process classes are available for executing and communicating with external programs. With an instance of the java.lang.ProcessBuilder class, it can execute an external program and return an instance of a subclass of java.lang.Process. The class Process provides methods for performing input from the process, performing output to the process, waiting for the process to complete, checking the exit status of the process, and destroying (killing) the process.

public class ProcessBuildDemo { 
    public static void main(String [] args) throws IOException {

        String[] command = {"CMD", "/C", "dir"};
        ProcessBuilder probuilder = new ProcessBuilder( command );
        //You can set up your work directory
        probuilder.directory(new File("c:\\xyzwsdemo"));

        Process process = probuilder.start();

        //Read out dir output
        InputStream is = process.getInputStream();
        InputStreamReader isr = new InputStreamReader(is);
        BufferedReader br = new BufferedReader(isr);
        String line;
        System.out.printf("Output of running %s is:\n",
                Arrays.toString(command));
        while ((line = br.readLine()) != null) {
            System.out.println(line);
        }

        //Wait to get exit value
        try {
            int exitValue = process.waitFor();
            System.out.println("\n\nExit Value is " + exitValue);
        } catch (InterruptedException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
}

I had success with this code:

ProcessBuilder pb = new ProcessBuilder(command);    
logger.debug(String.join(" ",pb.command().toArray(new String[0])));

You could set the directory from where the command to be executed

    List<String> cmds = Arrays.asList("cmd.exe", "/C", "start", "java", "-mx4g", "-cp", "*", "edu.stanford.nlp.pipeline.StanfordCoreNLPServer");
    ProcessBuilder builder = new ProcessBuilder(cmds);
    builder.directory(new File("D:/stanford-corenlp-full-2015-12-09"));
    Process proc = builder.start();

UPDATE as requested in comments

    OutputStream out = proc.getOutputStream();
    new Thread(() -> {
        try (BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(out))) {
            bw.write("[command here]");
            bw.flush();
        } catch (IOException ioe) {
            ioe.printStackTrace();
        }

    }).start();

Windows has no bash, so you have to use "CMD" (command). "bash" is being used for unix-systems.

This should work on Windows :

final Process exec = new ProcessBuilder("CMD", "/C", query).start();

if you want a nice example on how to use the ProcessBuilder in Windows : External programs using Java ProcessBuilder class

Your approaches are equivalent to calling ls with the specified arguments. In Bash notation, what you're running is:

ls ';' pwd
ls '&&' pwd

If you want ls and pwd to be run as separate commands, you can use Bash (or another shell language) to wrap them into a single command:

bash -c 'ls ; pwd'

which you can call this way:

ProcessBuilder processBuilder = new ProcessBuilder("bash", "-c", "ls ; pwd");