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

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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);

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