Running Bash commands in Java

You start a new process with Runtime.exec(command). Each process has a working directory. This is normally the directory in which the parent process was started, but you can change the directory in which your process is started.

I would recommend to use ProcessBuilder

ProcessBuilder pb = new ProcessBuilder("ls");
pb.inheritIO();
pb.directory(new File("bin"));
pb.start();

If you want to run multiple commands in a shell it would be better to create a temporary shell script and run this.

public void executeCommands() throws IOException {

    File tempScript = createTempScript();

    try {
        ProcessBuilder pb = new ProcessBuilder("bash", tempScript.toString());
        pb.inheritIO();
        Process process = pb.start();
        process.waitFor();
    } finally {
        tempScript.delete();
    }
}

public File createTempScript() throws IOException {
    File tempScript = File.createTempFile("script", null);

    Writer streamWriter = new OutputStreamWriter(new FileOutputStream(
            tempScript));
    PrintWriter printWriter = new PrintWriter(streamWriter);

    printWriter.println("#!/bin/bash");
    printWriter.println("cd bin");
    printWriter.println("ls");

    printWriter.close();

    return tempScript;
}

Of course you can also use any other script on your system. Generating a script at runtime makes sometimes sense, e.g. if the commands that are executed have to change. But you should first try to create one script that you can call with arguments instead of generating it dynamically at runtime.

It might also be reasonable to use a template engine like velocity if the script generation is complex.

EDIT

You should also consider to hide the complexity of the process builder behind a simple interface.

Separate what you need (the interface) from how it is done (the implementation).

public interface FileUtils {
    public String[] listFiles(String dirpath);
}

You can then provide implementations that use the process builder or maybe native methods to do the job and you can provide different implementations for different environments like linux or windows.

Finally such an interface is also easier to mock in unit tests.