I have an issue I'm trying to resolve. When I perform an xslt transform in the XSLT Debugger, the output is what I expect. When I execute a transform with the command line: java org.apache.xalan.xslt.Process -in applications\InputTemplate.xml -xsl configxsl\transformer.xsl -out applications\Output.xml the output is not the same. In oXygen, I've specified InputTemplate.xml as the XML, transformer.xsl as the XSL (both open in buffers) and Xalan. The difference I'm seeing is that in the debugger, an XInclude is being included (the output window shows the combined document, and properly transformed. This is what I want). The output when run from the command line leaves the XInclude element alone, but otherwise properly transforms the document. So does oXygen just process in-memory? Is there a way to see the equivalent command line? Thanks.