public Class CopyAndWrite {

        public static final String SOURCES = "D:\\sources";
        public static final String TARGET = "D:\\target";

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

            Path startingDir = Paths.get(SOURCES);
    
            Files.walkFileTree(startingDir, new FindJavaVisitor());
        }

        private static class FindJavaVisitor extends SimpleFileVisitor<Path> {

            @Override
            public FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) throws IOException {
                if (!StringUtils.equals(dir.toString(), SOURCES)) {
                    Path targetPath = Paths.get(TARGET + dir.toString().substring(SOURCES.length()));
                    if (!Files.exists(targetPath)) {
                        Files.createDirectory(targetPath);
                    }
                }
                return FileVisitResult.CONTINUE;
            }

            @Override
            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                Path targetPath = Paths.get(TARGET + file.toString().substring(SOURCES.length()));
                copyFile(targetPath, Files.readAllBytes(file));

                return FileVisitResult.CONTINUE;
            }
        }

        private static void copyFile (Path path,byte[] bytes){
            // write file
            try {
                Files.write(path, bytes);
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    }