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Probably due to a bug in the path resolution, the XHTML Basic/MP validation isn't done properly when the deploy.jar is run from a different directly than where it was built; see: http://www.w3.org/mid/1200302367.7038.374.camel@localhost
I've modified build.xml so that at least the dtd directory gets included in the deploy.jar. This hasn't fixed the problem yet since we need to tell the Catalog to look into the classpath (and not only on the filesystem), the same way it is done for the XSLTs.
http://lists.w3.org/Archives/Public/public-mobileok-checker/2008Jan/0086.html