Writing to separate XML files

I'm not too familiar with XML yet, so I don't know what its called, but you know how you can "include" another XML file in this fashion:
<?xml version="1.0"?>
<!DOCTYPE configuration SYSTEM "my.dtd" [
  <!ENTITY include SYSTEM "include.xml">
]>
<root>
  &include;
</root>... and all the stuff in include.xml gets essentially copied into yours whenever the file is read. Well how can I generate a file that looks like this. I basically want to be able to choose which nodes underneath the root node I can put in separate files. I'm doing this by converting a DOM to XML with this code...
         Document d = MY_DOCUMENT;
         DOMSource domSource = new DOMSource(d);
     TransformerFactory tf = TransformerFactory.newInstance();
     tf.setAttribute("indent-number",4);
     Transformer transformer = tf.newTransformer();
     transformer.setOutputProperty(OutputKeys.METHOD, "xml");
     transformer.setOutputProperty(OutputKeys.ENCODING,"ISO-8859-1");
     transformer.setOutputProperty(OutputKeys.INDENT, "yes");
     transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM,"ems.dtd");
     FileOutputStream fileOut = new FileOutputStream(filename);
     transformer.transform(domSource, new StreamResult(new OutputStreamWriter(fileOut,"utf-8")));
     fileOut.close();

You can also use commands like bcp withT-SQL  query to get the shredded XML values saved as separate xml files. You've xpath function like query() available which will shred out parts of XML from your main column
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