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Question: There seems to be a bug related to uncategorized articles.  If I create such an article, then link to it via menu, then unpublished the menu, but request the link via an article item, it inserts the site name.  It looks ugly and does NOT follow the format of the rest of the site.

Answer:  Yes, this is a bit annoying.  This is what you can do.  Create an MENU called UNCATEGORIZED, then move the link there and leave it published.  When you create the menu, it will also create a MODULE.  Just don't publish the module anywhere. This should resolve the problem.