【追加】
assets\public_html
assets\js\jquery.min.js
install\actionsフォルダ
install\assets\chunks\mm_rules.tpl
manager\includes\upgrades.php
manager\media\captchaフォルダ
【削除】
assets\js\jqueryフォルダ
assets\js\getjs.php
install\action.connection.php
install\action.install.php
install\action.language.php
install\action.mode.php
install\action.options.php
install\action.summary.php
install\assets\chunks\mm_demo_rules.tpl

manager\includes\localeフォルダ
manager\includes\noisesフォルダ
manager\includes\sniffフォルダ
manager\includes\ttfフォルダ
manager\includes\browsercheck.inc.php
manager\includes\veriword.php
manager\includes\extenders\getUserData.extender.php

manager\media\browser\mcpuk\connectors\php\Docs\AuthenticationHandlers.txt

manager\media\ImageEditor\Classes\IM.php
manager\media\ImageEditor\Classes\NetPBM.php
manager\media\ImageEditor\Classes\Thumbnail.php

manager\media\script\bin
【変更】

index.php
sample.htaccess

assets\plugins\managermanager\mm.inc.php
assets\plugins\managermanager\functions\tabs.inc.php
assets\plugins\managermanager\widgets\ddsetfieldvalue\ddsetfieldvalue.php
assets\plugins\managermanager\widgets\ddsetfieldvalue\ddsetfieldvalue.php

assets\plugins\qm\qm.inc.php

assets\snippets\ditto\debug\modxDebugConsole.class.php
assets\snippets\ditto\extenders\summary.extender.inc.php
assets\snippets\eform\eform.inc.php
assets\snippets\weblogin\websignup.inc.php

assets\templates\xray\content.css
assets\templates\xray\content.css

assets\upgradephp\upgrade.php

install\functions.php
install\index.php
install\instprocessor.php
install\setup.info.php
install\setup.sql
install\style.css

install\assets\chunks\login.tpl

install\assets\plugins\manager_tpl.tpl
install\assets\plugins\mgrmgr.tpl
install\assets\plugins\qm.tpl
install\assets\snippets\eform.tpl
install\assets\templates\xray.tpl

install\lang\english.inc.php

manager\actions\bkmanager.static.php
manager\actions\eventlog.dynamic.php
manager\actions\export_site.static.php
manager\actions\files.dynamic.php
manager\actions\import_site.static.php
manager\actions\modules.static.php
manager\actions\mutate_content.dynamic.php
manager\actions\mutate_htmlsnippet.dynamic.php
manager\actions\mutate_module.dynamic.php
manager\actions\mutate_module_resources.dynamic.php
manager\actions\mutate_plugin.dynamic.php
manager\actions\mutate_settings.dynamic.php
manager\actions\mutate_snippet.dynamic.php
manager\actions\mutate_templates.dynamic.php
manager\actions\mutate_tmplvars.dynamic.php
manager\actions\resource_selector.static.php
manager\actions\resources.static.php
manager\actions\role_management.static.php
manager\actions\user_management.static.php
manager\actions\web_user_management.static.php

manager\frames\1.php
manager\frames\nodes.php

manager\includes\accesscontrol.inc.php
manager\includes\config_check.inc.php
manager\includes\document.parser.class.inc.php
manager\includes\initialize.inc.php
manager\includes\log.class.inc.php
manager\includes\protect.inc.php
manager\includes\tmplvars.commands.inc.php
manager\includes\tmplvars.format.inc.php
manager\includes\version.inc.php

manager\includes\controls\datagrid.class.php
manager\includes\controls\datasetpager.class.php
manager\includes\controls\modxmailer.inc.php
manager\includes\lang\english.inc.php
manager\includes\lang\japanese-utf8.inc.php

manager\media\browser\mcpuk\connectors\php\Commands\FileUpload.php
manager\media\browser\mcpuk\connectors\php\Commands\GetFolders.php
manager\media\browser\mcpuk\connectors\php\Commands\GetUploadProgress.php

manager\media\rss\rss_cache.inc
manager\media\rss\rss_fetch.inc

manager\media\style\MODxCarbon\style.css
manager\media\style\MODxCarbon\style.php

manager\processors\cache_sync.class.processor.php
manager\processors\save_htmlsnippet.processor.php
manager\processors\save_module.processor.php
manager\processors\save_settings.processor.php
manager\processors\save_user.processor.php
入れてみたら、「ファイル管理機能の対象ディレクトリのパス設定が正しくありません」と出るエラーがでたので、
http://forum.modx.jp/viewtopic.php?f=7&t=826&start=0
を見て、調べました。

ここに記事のあったBindings機能の有効無効のpluginをオフにすることで問題はなくなりましたが、Bindings機能ってなんでしょうか。

「Dreamweaverなどで作ったhtmlファイルをそのままテンプレートにする」というようなときに利用するとあります。http://modx.jp/docs/tips/other.html

ひとまず、今は使わないのでpluginをオフにしておこうと思います。