Here is the configuration from the extension that I wrote that “injected” javascript into the publish dialog, maybe you should give it a chance to see if it also includes any css:
<?xml version="1.0"?>
<Configuration xmlns="http://www.sdltridion.com/2009/GUI/Configuration/Merge" xmlns:cfg="http://www.sdltridion.com/2009/GUI/Configuration" xmlns:ext="http://www.sdltridion.com/2009/GUI/extensions" xmlns:cmenu="http://www.sdltridion.com/2009/GUI/extensions/ContextMenu">
<resources cache="true">
<cfg:extensiongroups>
<cfg:extensiongroup name="Company.Extensions.Group">
<cfg:extension target="Tridion.Web.UI.Editors.CME.Views.Popups.Publish">
<cfg:insertafter>Company.Extensions.Resources</cfg:insertafter>
</cfg:extension>
</cfg:extensiongroup>
</cfg:extensiongroups>
<cfg:groups>
<cfg:group name="Company.Extensions.Resources">
<cfg:fileset>
<cfg:file type="script">/js/SelectRollbackFailure.js</cfg:file>
<cfg:file type="script">/js/NoPublishItemWarning.js</cfg:file>
</cfg:fileset>
</cfg:group>
</cfg:groups>
</resources>
<definitionfiles/>
<extensions>
<ext:dataextenders/>
<ext:editorextensions />
</extensions>
<commands />
<contextmenus/>
<localization></localization>
<settings>
<defaultpage />
<navigatorurl />
<editurls/>
<listdefinitions/>
<itemicons/>
<theme>
<path></path>
<resourcegroup />
</theme>
<resourceextensions>
<resourceextension>Company.Extensions.Group</resourceextension>
</resourceextensions>
<customconfiguration></customconfiguration>
</settings>
</Configuration>
You will need to change this part:
<cfg:extension target="Tridion.Web.UI.Editors.CME.Views.Popups.Publish">
Here you want to include elements. If this is not entirely correct, or you need an explanation, let me know.
ps I also suspect that some empty nodes may be deleted :)
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