The code intended to replace an existing string with a string provided by user.its not working through CMD

The following code intended to replace an existing string with a user provided string.its not working properly through command prompt though its working fine in MyEclipse.

The following method will read all the files in a directory/sub directories and replace the source string with destination string and rewrite the whole file.

public static void CopyandWriteall(String directoryName, String source,
        String destination) {
    File directory = new File(directoryName);
    // get all the files from a directory
    File[] fList = directory.listFiles();
    int changed_count = 0;
    int total_count = 0;
    int filechange_count = 0;

    for (File file : fList) {
        filechange_count = 0;
        newXml = "";
        if (file.isFile()) {
            String filePath = file.getAbsolutePath();
            // System.out.println(filePath);
            String fileName = filePath
                    .substring(filePath.lastIndexOf("\\"));
            String fileExtension = fileName.substring(fileName
                    .lastIndexOf(".") + 1);
            BufferedReader br = null;
            String CurrentLine;

            try {
                br = new BufferedReader(new FileReader(file));
                while ((CurrentLine = br.readLine()) != null) {

                    if (CurrentLine.contains(source)) {
                        filechange_count++;
                        CurrentLine = CurrentLine.replaceAll(source,
                                destination);
                        // changed_count++;
                        // filechange_count++;

                    }

                    newXml = CurrentLine + "\n";

                }
                System.out.println("filePath====" + filePath + fileName
                        + "=======filechange_count===" + filechange_count);
                File NewXmlfile = new File(filePath);
                // System.out.println(directoryName+"\\updatedFiles"
                // +fileName);
                FileWriter fw = new FileWriter(NewXmlfile.getAbsoluteFile());
                BufferedWriter bw = new BufferedWriter(fw);
                bw.write(newXml);
                bw.close();

            } catch (IOException e) {
                e.printStackTrace();
            } finally {
                try {
                    br.close();
                } catch (IOException e) {

                    e.printStackTrace();
                }
            }

        }

        else if (file.isDirectory()) {
            CopyandWriteall(file.getAbsolutePath(), source, destination,
                    LogPath);
            System.out.println(file.getAbsolutePath());
        }
        // System.out.println(newXml);
        total_count++;
    }

}

}