Deciding how to structure documentation at the command level has been really straightforward thanks to such things as unix man pages, javadoc (although I hate automated documentation schemes) and the web. However it becomes a bit more difficult when you have to document a system. Most system documentation provides a roadmap of the commands, command pages and data dictionary. Developer documentation usually describes the routines/classes with appropriate args but not much algorithmic description or system description.
What do you consider an acceptable framework for system documentation. Can you cite any examples that are accessible on the web?
Comments please! Thanks!