Jira web application's library xml-apis-1.3.04.jar duplicates classes from JRE

Jira standalone webapplication contains xml-apis-1.3.04.jar that contains classes found in JDK 7 and JDK 8. Duplicate classes relate to XML processing such as javax.xml.namespace.QName, org.w3c.dom.Entity, org.xml.sax.Attributes and many others.

Jar location in jira standalone package: atlassian-jira\WEB-INF\lib\xml-apis-1.3.04.jar

According to Tomcat documentation (http://tomcat.apache.org/tomcat-7.0-doc/class-loader-howto.html) "Classes which are part of the JRE base classes cannot be overridden."

Duplication of classes resulted for me in java.lang.NoClassDefFoundError and java.lang.LinkageError in my plugin.
I deleted xml-apis-1.3.04.jar from my standalone jira and it fixed the problem.

Please delete xml-apis-1.3.04.jar from jira distribution.