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When using the core upgrade function, introduced with Version 2.7, some old files, which are no longer included with the latest release, will be deleted. The list of files to be deleted is in the wp-admin/includes/update-core.php file.
In addition to the files to be deleted, all other core files are replaced with the newer versions. If you have made modifications to any core files, including the WordPress Default theme files, you'll need to insure they are backed up before attempting the core upgrade. After the upgrade, you'll have to retrofit the modifications to the new core files again. Simply re-using the old modified files is NOT recommended.
$_old_files = array( 'wp-admin/bookmarklet.php', 'wp-admin/css/upload.css', 'wp-admin/css/upload-rtl.css', 'wp-admin/css/press-this-ie.css', 'wp-admin/css/press-this-ie-rtl.css', 'wp-admin/edit-form.php', 'wp-admin/link-import.php', 'wp-admin/images/box-bg-left.gif', 'wp-admin/images/box-bg-right.gif', 'wp-admin/images/box-bg.gif', 'wp-admin/images/box-butt-left.gif', 'wp-admin/images/box-butt-right.gif', 'wp-admin/images/box-butt.gif', 'wp-admin/images/box-head-left.gif', 'wp-admin/images/box-head-right.gif', 'wp-admin/images/box-head.gif', 'wp-admin/images/heading-bg.gif', 'wp-admin/images/login-bkg-bottom.gif', 'wp-admin/images/login-bkg-tile.gif', 'wp-admin/images/notice.gif', 'wp-admin/images/toggle.gif', 'wp-admin/images/comment-stalk-classic.gif', 'wp-admin/images/comment-stalk-fresh.gif', 'wp-admin/images/comment-stalk-rtl.gif', 'wp-admin/images/comment-pill.gif', 'wp-admin/images/del.png', 'wp-admin/images/media-button-gallery.gif', 'wp-admin/images/media-buttons.gif', 'wp-admin/images/tail.gif', 'wp-admin/images/gear.png', 'wp-admin/images/tab.png', 'wp-admin/images/postbox-bg.gif', 'wp-admin/includes/upload.php', 'wp-admin/js/dbx-admin-key.js', 'wp-admin/js/link-cat.js', 'wp-admin/js/forms.js', 'wp-admin/js/upload.js', 'wp-admin/js/set-post-thumbnail-handler.js', 'wp-admin/js/set-post-thumbnail-handler.dev.js', 'wp-admin/js/page.js', 'wp-admin/js/page.dev.js', 'wp-admin/js/slug.js', 'wp-admin/js/slug.dev.js', 'wp-admin/profile-update.php', 'wp-admin/templates.php', 'wp-includes/images/audio.png', 'wp-includes/images/css.png', 'wp-includes/images/default.png', 'wp-includes/images/doc.png', 'wp-includes/images/exe.png', 'wp-includes/images/html.png', 'wp-includes/images/js.png', 'wp-includes/images/pdf.png', 'wp-includes/images/swf.png', 'wp-includes/images/tar.png', 'wp-includes/images/text.png', 'wp-includes/images/video.png', 'wp-includes/images/zip.png', 'wp-includes/js/dbx.js', 'wp-includes/js/fat.js', 'wp-includes/js/list-manipulation.js', 'wp-includes/js/jquery/jquery.dimensions.min.js', 'wp-includes/js/tinymce/langs/en.js', 'wp-includes/js/tinymce/plugins/autosave/editor_plugin_src.js', 'wp-includes/js/tinymce/plugins/autosave/langs', 'wp-includes/js/tinymce/plugins/directionality/images', 'wp-includes/js/tinymce/plugins/directionality/langs', 'wp-includes/js/tinymce/plugins/inlinepopups/css', 'wp-includes/js/tinymce/plugins/inlinepopups/images', 'wp-includes/js/tinymce/plugins/inlinepopups/jscripts', 'wp-includes/js/tinymce/plugins/paste/images', 'wp-includes/js/tinymce/plugins/paste/jscripts', 'wp-includes/js/tinymce/plugins/paste/langs', 'wp-includes/js/tinymce/plugins/spellchecker/classes/HttpClient.class.php', 'wp-includes/js/tinymce/plugins/spellchecker/classes/TinyGoogleSpell.class.php', 'wp-includes/js/tinymce/plugins/spellchecker/classes/TinyPspell.class.php', 'wp-includes/js/tinymce/plugins/spellchecker/classes/TinyPspellShell.class.php', 'wp-includes/js/tinymce/plugins/spellchecker/css/spellchecker.css', 'wp-includes/js/tinymce/plugins/spellchecker/images', 'wp-includes/js/tinymce/plugins/spellchecker/langs', 'wp-includes/js/tinymce/plugins/spellchecker/tinyspell.php', 'wp-includes/js/tinymce/plugins/wordpress/images', 'wp-includes/js/tinymce/plugins/wordpress/langs', 'wp-includes/js/tinymce/plugins/wordpress/popups.css', 'wp-includes/js/tinymce/plugins/wordpress/wordpress.css', 'wp-includes/js/tinymce/plugins/wphelp', 'wp-includes/js/tinymce/themes/advanced/css', 'wp-includes/js/tinymce/themes/advanced/images', 'wp-includes/js/tinymce/themes/advanced/jscripts', 'wp-includes/js/tinymce/themes/advanced/langs', 'wp-includes/js/tinymce/tiny_mce_gzip.php', 'wp-includes/js/wp-ajax.js', 'wp-admin/admin-db.php', 'wp-admin/cat.js', 'wp-admin/categories.js', 'wp-admin/custom-fields.js', 'wp-admin/dbx-admin-key.js', 'wp-admin/edit-comments.js', 'wp-admin/install-rtl.css', 'wp-admin/install.css', 'wp-admin/upgrade-schema.php', 'wp-admin/upload-functions.php', 'wp-admin/upload-rtl.css', 'wp-admin/upload.css', 'wp-admin/upload.js', 'wp-admin/users.js', 'wp-admin/widgets-rtl.css', 'wp-admin/widgets.css', 'wp-admin/xfn.js', 'wp-includes/js/tinymce/license.html', 'wp-admin/cat-js.php', 'wp-admin/edit-form-ajax-cat.php', 'wp-admin/execute-pings.php', 'wp-admin/import/b2.php', 'wp-admin/import/btt.php', 'wp-admin/import/jkw.php', 'wp-admin/inline-uploading.php', 'wp-admin/link-categories.php', 'wp-admin/list-manipulation.js', 'wp-admin/list-manipulation.php', 'wp-includes/comment-functions.php', 'wp-includes/feed-functions.php', 'wp-includes/functions-compat.php', 'wp-includes/functions-formatting.php', 'wp-includes/functions-post.php', 'wp-includes/js/dbx-key.js', 'wp-includes/js/tinymce/plugins/autosave/langs/cs.js', 'wp-includes/js/tinymce/plugins/autosave/langs/sv.js', 'wp-includes/js/tinymce/themes/advanced/editor_template_src.js', 'wp-includes/links.php', 'wp-includes/pluggable-functions.php', 'wp-includes/template-functions-author.php', 'wp-includes/template-functions-category.php', 'wp-includes/template-functions-general.php', 'wp-includes/template-functions-links.php', 'wp-includes/template-functions-post.php', 'wp-includes/wp-l10n.php', 'wp-admin/import-b2.php', 'wp-admin/import-blogger.php', 'wp-admin/import-greymatter.php', 'wp-admin/import-livejournal.php', 'wp-admin/import-mt.php', 'wp-admin/import-rss.php', 'wp-admin/import-textpattern.php', 'wp-admin/quicktags.js', 'wp-images/fade-butt.png', 'wp-images/get-firefox.png', 'wp-images/header-shadow.png', 'wp-images/smilies', 'wp-images/wp-small.png', 'wp-images/wpminilogo.png', 'wp.php', 'wp-includes/gettext.php', 'wp-includes/streams.php' );
wp-content/themes/default/attachment.php
wp-content/themes/default/images/kubrickbg.jpg
wp-content/plugins/markdown.php
wp-content/plugins/textile1.php