I'm using Doxygen at work. I noticed that if you document a namespace such as foo, then the documentation for that namespace goes into a file called namespacefoo.html. The higher level file that contains the list of all documented namespaces in the project is called namespaces.html. Guess what happens when you document a namespace called s? Doxygen overwrites the index of all namespaces with the documentation for namespace s, and poof, no more index.

(I don't actually have a namespace called s; I was just curious what would happen when I intentionally tried to break things.)