Location of files

I recently installed 2.3.1 on my blog, but it appears that in my theme folder there are some extra files that shouldn’t be there. Can somebody tell me where these files actually belong? The files are:

wp-rss2.php
xmlrpc.php
wp-app.php
wp-mail.php
wp-config-sample.php
wp-pass.php
wp-commentsrss2.php
wp-blog-header.php
wp-settings.php
wp-rdf.php
wp-feed.php
wp-trackback.php
wp-links-opml.php
wp-comments-post.php
wp-register.php
wr-rss.php
wp-cron.php
wp-login.php
wp-atom.php

Again, they are appearing in my actual theme folder, and it seems it’s wreaking a little havoc with my blog.

Thank you.