Section 46.3 Modular Source Files
If you use the 
<xi:include> mechanism for modular source files, you must process your source slightly differently.Add the switch 
-xinclude to your invocation of xsltproc, just after xsltproc, but before the filenames for the stylesheet and the top-level source file.  Note that for some versions of xsltproc it might be necessary to use two dashes for the switch, --xinclude. So now a typical invocation (using one dash) might look likexsltproc -xinclude xsl/pretext-html.xsl ~/books/aota/animals.xml
It is easy to forget the 
-xinclude switch.  Empty output, or cryptic error messages, are your first clue to this simple, but common, mistake.