The problem is being caused by a JAR file whose MANIFEST.MF file contains a value for the Extension-List attribute that Tomcat doesn't like. Tomcat expects this attribute's value to be a space-separated list of extension names (see the ManifestResource source), but it appears one of your JARs has the comma-separated list dom4j-core,jdom,xml-apis,xerces,junit instead. There are no spaces in this list, so Tomcat thinks it's all one big extension name.
Extension names are also used to prefix names of further attributes within the manifest. For example, here's part of a valid manifest:
Extension-List: ant qdox commons-attributes-api javadoc ant-Extension-Name: ant ant-Implementation-Version: 1.5 ant-Implementation-URL: http://www.ibiblio.org/maven/ant/jars/ant-1.5. jar qdox-Extension-Name: qdox qdox-Implementation-Version: 1.5
Attribute names can only contain letters, numbers, hyphens and underscores, and so extension names must also follow the same rules. An extension name with a comma in it is clearly not valid, and this is why you are getting the exception above.
I've had a look at the official JAR file specification, but that appears not to state how these extension names should be delimited.
I can't say which JAR has this comma-separated Extension-List attribute in its manifest. However, I would check the JAR files within the latest versions of XMLBeans and Saxon first. If your project worked before the upgrade, then it's likely that the problem has been caused by something that has changed recently.
The fix is of course to edit the offending manifest file to use spaces instead of commas in its Extension-List attribute.
Good luck!