Patch file onvdl.diff below. You would run:
patch -p1 <onvdl.diff
in the directory into which src.zip was extracted. The diff contains CRLF line endings, which might get lost if you copy and paste from the web browser.
onvdl.diff:
diff -Naur src/com/oxygenxml/validate/isoschematron/SaxonSchemaReaderFactory.java newsrc/com/oxygenxml/validate/isoschematron/SaxonSchemaReaderFactory.java
--- src/com/oxygenxml/validate/isoschematron/SaxonSchemaReaderFactory.java	2007-04-03 23:03:40.000000000 +0000
+++ newsrc/com/oxygenxml/validate/isoschematron/SaxonSchemaReaderFactory.java	2007-09-06 18:54:36.000000000 +0000
@@ -1,11 +1,12 @@
 package com.oxygenxml.validate.isoschematron;
 
-import com.icl.saxon.TransformerFactoryImpl;
-
 import javax.xml.transform.TransformerFactory;
 
+import net.sf.saxon.TransformerFactoryImpl;
+
 public class SaxonSchemaReaderFactory extends SchematronSchemaReaderFactory {
   public TransformerFactory newTransformerFactory() {
-    return new TransformerFactoryImpl();
+	  TransformerFactory tf = new TransformerFactoryImpl();
+    return tf;
   }
 }
diff -Naur src/com/oxygenxml/validate/isoschematron/SchemaReaderImpl.java newsrc/com/oxygenxml/validate/isoschematron/SchemaReaderImpl.java
--- src/com/oxygenxml/validate/isoschematron/SchemaReaderImpl.java	2007-04-03 23:26:30.000000000 +0000
+++ newsrc/com/oxygenxml/validate/isoschematron/SchemaReaderImpl.java	2007-09-06 18:54:36.000000000 +0000
@@ -17,6 +17,9 @@
 import com.thaiopensource.xml.sax.DraconianErrorHandler;
 import com.thaiopensource.xml.sax.ForkContentHandler;
 import com.thaiopensource.xml.sax.XMLReaderCreator;
+
+import net.sf.saxon.FeatureKeys;
+
 import org.xml.sax.Attributes;
 import org.xml.sax.ContentHandler;
 import org.xml.sax.ErrorHandler;
@@ -85,10 +88,11 @@
   private void initTransformerFactory(TransformerFactory factory) {
     String name = factory.getClass().getName();
     try {
-      if (name.equals("com.icl.saxon.TransformerFactoryImpl"))
-        factory.setAttribute("
http://icl.com/saxon/feature/linenumbering",
+      if (name.equals("net.sf.saxon.TransformerFactoryImpl")) {
+        factory.setAttribute("
http://saxon.sf.net/feature/linenumbering",
                              Boolean.TRUE);
-      else if (name.equals("org.apache.xalan.processor.TransformerFactoryImpl")) {
+    	factory.setAttribute(FeatureKeys.VERSION_WARNING, false);
+    } else if (name.equals("org.apache.xalan.processor.TransformerFactoryImpl")) {
         // Try both the documented URI and the URI that the code expects.
         try {
           // This is the URI that the code expects.
diff -Naur src/com/thaiopensource/validate/schematron/SaxonSchemaReaderFactory.java newsrc/com/thaiopensource/validate/schematron/SaxonSchemaReaderFactory.java
--- src/com/thaiopensource/validate/schematron/SaxonSchemaReaderFactory.java	2006-11-15 21:07:04.000000000 +0000
+++ newsrc/com/thaiopensource/validate/schematron/SaxonSchemaReaderFactory.java	2007-09-06 18:54:36.000000000 +0000
@@ -1,11 +1,12 @@
 package com.thaiopensource.validate.schematron;
 
-import com.icl.saxon.TransformerFactoryImpl;
-
 import javax.xml.transform.TransformerFactory;
 
+import net.sf.saxon.TransformerFactoryImpl;
+
 public class SaxonSchemaReaderFactory extends SchematronSchemaReaderFactory {
   public TransformerFactory newTransformerFactory() {
-    return new TransformerFactoryImpl();
+	  TransformerFactory tf = new TransformerFactoryImpl();
+    return tf;
   }
 }
diff -Naur src/com/thaiopensource/validate/schematron/SchemaReaderImpl.java newsrc/com/thaiopensource/validate/schematron/SchemaReaderImpl.java
--- src/com/thaiopensource/validate/schematron/SchemaReaderImpl.java	2007-01-16 20:24:48.000000000 +0000
+++ newsrc/com/thaiopensource/validate/schematron/SchemaReaderImpl.java	2007-09-06 18:54:36.000000000 +0000
@@ -17,6 +17,9 @@
 import com.thaiopensource.xml.sax.DraconianErrorHandler;
 import com.thaiopensource.xml.sax.ForkContentHandler;
 import com.thaiopensource.xml.sax.XMLReaderCreator;
+
+import net.sf.saxon.FeatureKeys;
+
 import org.xml.sax.Attributes;
 import org.xml.sax.ContentHandler;
 import org.xml.sax.ErrorHandler;
@@ -85,10 +88,11 @@
   private void initTransformerFactory(TransformerFactory factory) {
     String name = factory.getClass().getName();
     try {
-      if (name.equals("com.icl.saxon.TransformerFactoryImpl"))
-        factory.setAttribute("
http://icl.com/saxon/feature/linenumbering",
+      if (name.equals("net.sf.saxon.TransformerFactoryImpl")) {
+        factory.setAttribute("
http://saxon.sf.net/feature/linenumbering",
                              Boolean.TRUE);
-      else if (name.equals("org.apache.xalan.processor.TransformerFactoryImpl")) {
+      	factory.setAttribute(FeatureKeys.VERSION_WARNING, false);
+      } else if (name.equals("org.apache.xalan.processor.TransformerFactoryImpl")) {
         // Try both the documented URI and the URI that the code expects.
         try {
           // This is the URI that the code expects.