Clarification on release notes needed

The look and feel of your JSPWiki instance is almost exclusively driven by
the JSP templates and CSS files in the template directory. The release notes
recommends us to just copy over the new jar files, the top-level jsp files,
and the default template. I assume that this is from the distribution .war
file to the installed webapp. If we do this, we obviously loose our changes.

Am I misreading these notes?
I am also assuming that the old and new files need to be synchronized. Where
can I find out which files in each new release have been changed?