When I run frameworks/schematron/impl/schematronDispatcher.xsl against a schematron file that contains xsl:include elements, relative paths in the href attributes on the xsl:include elements are only correct if the result document happens to be in the same directory as the original schematron.
For example, say I have the following schematron that uses sch:extends. In the schematron that we're extending, there are xsl:include elements with paths that are relative to cals.sch. In the result of schematronDispatcher.xsl, the xsl:include/@href values will not be correct because they are copied verbatim from cals.sch:
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<sch:schema xmlns:sch="http://purl.oclc.org/dsdl/schematron" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" queryBinding="xslt2"
<!-- Other stuff -->