When building XEP 4.9 Cocoon connector on my local (Linux) machine I had to install ant and junit from ubuntu repositories otherwise builds failed. I had been setting the $junit variable to point to a standalone instance that worked for me before but it bailed this time. Once set up the build (ant make.jar) went fine. It still wants to install the same manky saxon.jar as it did before, and that still screws Cocoon on initialization, so out it goes. Instead of running the "installer", just copy the jars xep.jar, XEPSerializer.jar and xt.jar to the {$COCOON_HOME}/WEB-INF/lib/ directory and alter the root sitemap to load xep:

<!-- Customization: XEP -->
<map:serializer mime-type="application/pdf" name="fo2pdf"
src="com.renderx.xepx.cocoon.Serializer">
<parameter name="com.renderx.xep.CONFIG" type="string"
value="/complete/filesystem/path/to/xep.xml"/>
</map:serializer>
<map:serializer mime-type="application/postscript" name="fo2ps"
src="com.renderx.xepx.cocoon.Serializer">
<parameter name="com.renderx.xep.CONFIG" type="string"
value="/complete/filesystem/path/to/xep.xml"/>
</map:serializer>

Remember to change the name value for the FOP serializer or there will be a collision between xep and fop