I did a little more poking around, and it turns out that even though the woody template transformer mangles the xml document, the problem does not appear unless you run the document through the identity xslt transform.

Simple example:

test.xml
~~~~~~~~
<html xmlns="http://www.w3.org/1999/xhtml";>
<body>
Hello World
</body>
</html>

test.xsl
~~~~~~~~
<?xml version="1.0"?>
<xsl:stylesheet version="1.0"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform";
>
<xsl:template match="@*|node()" priority="-1">
<xsl:copy>
<xsl:apply-templates select="@*|node()"/>
</xsl:copy>
</xsl:template>
</xsl:stylesheet>

pipeline
~~~~~~~~
<map:match pattern="test">
  <map:generate src="test.xml"/>
  <map:transform type="woody"/>
  <map:transform src="test.xsl"/>
  <map:serialize/>
</map:match>

Will produce
~~~~~~~~~~~~
< xmlns="http://www.w3.org/1999/xhtml";>
<>
Hello World
</>
</>

But if you remove the woody transform or the xslt, you get
~~~~~~~~~~~~~~
<html xmlns="http://www.w3.org/1999/xhtml";>
<body>
Hello World
</body>
</html>



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