Jrju is a Perl application that "weaves hypertext 'notebooks' from plain text files." It's a bit like a wiki, but actually seems to have been developed before the idea of a wiki was conceived. It uses a special kind of markup. Its files are stored in plain text Links are automatically recognised. Jrju is also much more hierarchical than wiki. "Each notebook has a table of contents that serves as a top level index. Hierarchical indexes provide more specificity when needed. All available notes are listed somewhere in the hierarchy."
I am not recommending using it, since it appears rather dated. I gave it a try a long time ago.
No further comment!