Pretty-printing output from javax.xml.transform.Transformer with only standard java api (Indentation and Doctype positioning)

The missing part is the amount to indent. You can set the indentation and indent amount as follow:

transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
transformer.transform(xmlInput, xmlOutput);

A little util class as an example...

import org.apache.xml.serialize.XMLSerializer;

public class XmlUtil {

public static Document file2Document(File file) throws Exception {
    if (file == null || !file.exists()) {
        throw new IllegalArgumentException("File must exist![" + file == null ? "NULL"
                : ("Could not be found: " + file.getAbsolutePath()) + "]");
    }
    DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
    dbFactory.setNamespaceAware(true);
    return dbFactory.newDocumentBuilder().parse(new FileInputStream(file));
}

public static Document string2Document(String xml) throws Exception {
    InputSource src = new InputSource(new StringReader(xml));
    DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
    dbFactory.setNamespaceAware(true);
    return dbFactory.newDocumentBuilder().parse(src);
}

public static OutputFormat getPrettyPrintFormat() {
    OutputFormat format = new OutputFormat();
    format.setLineWidth(120);
    format.setIndenting(true);
    format.setIndent(2);
    format.setEncoding("UTF-8");
    return format;
}

public static String document2String(Document doc, OutputFormat format) throws Exception {
    StringWriter stringOut = new StringWriter();
    XMLSerializer serial = new XMLSerializer(stringOut, format);
    serial.serialize(doc);
    return stringOut.toString();
}

public static String document2String(Document doc) throws Exception {
    return XmlUtil.document2String(doc, XmlUtil.getPrettyPrintFormat());
}

public static void document2File(Document doc, File file) throws Exception {
    XmlUtil.document2String(doc, XmlUtil.getPrettyPrintFormat());
}

public static void document2File(Document doc, File file, OutputFormat format) throws Exception {
    XMLSerializer serializer = new XMLSerializer(new FileOutputStream(file), format);
    serializer.serialize(doc);
}
}

XMLserializer is provided by xercesImpl from the Apache Foundation. Here is the maven dependency:

<dependency>
    <groupId>xerces</groupId>
    <artifactId>xercesImpl</artifactId>
    <version>2.11.0</version>
</dependency>

You can find the dependency for your favourite build tool here: http://mvnrepository.com/artifact/xerces/xercesImpl/2.11.0.

You could probably prettify everything with an XSLT file. Google throws up a few results, but I can't comment on their correctness.