Saxon

In the net.sf.saxon.Configuration class in the two places where the ChainedResourceResolver is created, it should add the xml reader's entity resolver as the first resolver in the chain, otherwise the other resolver has the habit of returning a source even if it cannot resolve the reference and the xml reader's entity resolver would never get called. In the class ChainedEntityResolver on the net.sf.saxon.lib.ChainedEntityResolver.resolveEntity(String, String, String, String) method if the "first" and "second" are not EntityResolver2, but plain EntityResolver you could fallback to the EntityResolver API like:

    public InputSource resolveEntity(String name, String publicId, String baseURI, String systemId) throws SAXException, IOException {
        InputSource is = null;
        if (first instanceof EntityResolver2) {
            is = ((EntityResolver2) first).resolveEntity(name, publicId, baseURI, systemId);
        } else {
        	is = first.resolveEntity(publicId, systemId);
        }
        if (is == null) {
        	if(second instanceof EntityResolver2) {
            is = ((EntityResolver2) second).resolveEntity(name, publicId, baseURI, systemId);
          } else {
            is = second.resolveEntity(publicId, systemId);
          }
        }
        return is;
    }