This thread is for discussion of tools to help with documentation.
For documentation of java source files, we have javadoc: Sun's own document generator polardoc: an improved version by Tony Gee at the University of Alberta.
Both of these tools rely on the programmer embedding special tags into the comments to be most effective (@author, @version, etc) and then automagically generate HTML pages.
LeeDanielCrocker (in DocumentationFileFormat) has proposed that we skip HTML and move straight to XML. Participate in that discussion in DocumentationFileFormat.
A personal bias of mine is towards single-file sources. So I like DocLiterateProgramming --BillRehm