These parts of MKDoc should be made aware of groups:
Search — only list documents that people have permission to read.
RSS feeds — only list documents that people have permission to read.
These have been fixed, the newsletters are now ‘groups aware’ and the dynamic sitemap won't allow users to drill down through a restricted tree:
Email newsletters — only notify people about new documents that they have permission to read.
Sitemap — only list documents that people have permission to read.