Muy sencillamente podemos mover folders usando un script como este.

// the file we want to move
File file = new File("original.txt");
    
// the directory of destination
File folder = new File("newFolder");

File newPath = new File(folder, file.getName());
    
// Move file to new directory
boolean success = file.renameTo(newPath);
System.out.println("file moved ok: "   success);