为什么使用Java在文件的开头和结尾追加字符串后，xml文件无法正确对齐？

我已在XML File的开头和结尾添加了字符串。但是在得到结果后，对齐方式不正确。

我的XML文件：

        import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.Reader;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.w3c.dom.Text;
import org.xml.sax.SAXException;

import com.google.common.io.Resources;

import java.io.StringReader;
import java.io.StringWriter;
import java.net.URL;
import java.nio.charset.Charset;

import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.TransformerFactoryConfigurationError;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;

public class ModifyXMLFile {

    public static void main(String args[]) {

        try {
            // Point the file directory path here
            String directory = "C:\\Users\\n444479\\Desktop\\SA";
            int test = new File("C:\\Users\\n444479\\Desktop\\SA").listFiles().length;
            File[] files = new File(directory).listFiles();

            // Loop the file to run all the XML files
            for (int j = 0; j < test; j++) {
                System.out.println(files[j]);

                String filepathext = files[j].toString();

                DocumentBuilderFactory docFactory = DocumentBuilderFactory
                        .newInstance();
                DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
                Document doc = docBuilder.parse(filepathext);

                /*
                // XML file update starts here

                // 1.Add the attribute element with value between the two XML
                // Child elements



                 NodeList nodes = doc.getElementsByTagName("dummySegmentOne");
                 Text a = doc.createTextNode("value"); Element p =
                 doc.createElement("newNode"); p.appendChild(a);
                 nodes.item(0).getParentNode().insertBefore(p, nodes.item(0));


                // 2.Add the attribute element without value between the two XML
                // Child elements


                 NodeList nodesa =
                 doc.getElementsByTagName("customerLevelRegDocs"); Element q =
                 doc.createElement("dummySegmentOne");
                 nodesa.item(0).getParentNode().insertBefore(q,
                 nodesa.item(0));


                // 3.Rename the element in parent and child both using the JAXP
                // Parser
                */
                // XSLT File:

                String xsltResource = "C:\\Users\\n444479\\Desktop\\AB\\test.xml";

                StringWriter xmlResultResource = new StringWriter();

                Transformer xmlTransformer = TransformerFactory.newInstance().newTransformer(
                                new StreamSource(new File(xsltResource)));
                xmlTransformer.transform(new StreamSource(new File(filepathext)),new StreamResult(xmlResultResource));

                // XML file update end here

                // write the content into XML file
                TransformerFactory transformerFactory = TransformerFactory
                        .newInstance();
                Transformer transformer = transformerFactory.newTransformer();
                DOMSource source = new DOMSource(doc);
                StreamResult result = new StreamResult(new String(filepathext));
                transformer.transform(source, result);
                transformer.setOutputProperty(OutputKeys.INDENT, "yes");
                transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
                // Successful output once get it "Done"
                String output = xmlResultResource.getBuffer().toString();
                // Writing the transformed XML to a file
                FileWriter fileWriter = new FileWriter(filepathext);
                fileWriter.write(output);
                fileWriter.close();

                System.out.println("Done");

            }
        }
        // Exception handling
        catch (ParserConfigurationException pce) {
            pce.printStackTrace();
        } catch (TransformerException tfe) {
            tfe.printStackTrace();
        } catch (IOException ioe) {
            ioe.printStackTrace();
        } catch (SAXException sae) {
            sae.printStackTrace();
        }
    }

}

程序执行完字符串后，将正确附加该字符串，但是XML File的对齐方式发生了变化。

我得到的输出如下

<?xml version="1.0" encoding="UTF-8"?>{% from lxml import etree %}{% from StringIO import StringIO %}{% set tree = parse_xml(request_text) %}{% set namespaces = {'soapenv': 'http://schemas.xmlsoap.org/soap/envelope/',  'wbs': 'http://xml.ama.com/ws/2009/01/WBS_Session-2.0.xsd'}%}<soap:Envelope xmlns:xalan="http://xml.apache.org/xalan" xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/"><soap:Header><Session><SessionId>{{tree.xpath('//soapenv:Header/wbs:Session/wbs:SessionId', namespaces=namespaces)[0].text}}</SessionId><SequenceNumber>{{int(tree.xpath('//soapenv:Header/wbs:Session/wbs:SequenceNumber', namespaces=namespaces)[0].text)+1}}</SequenceNumber><SecurityToken>{{tree.xpath('//soapenv:Header/wbs:Session/wbs:SecurityToken', namespaces=namespaces)[0].text}}</SecurityToken></Session></soap:Header><soap:Body><reRoot><reNode> world</reNode></reRoot></soap:Body></soap:Envelope>

为什么文件没有被附加