<p>Pretty cool. I like the cross cutting especially. I had two ideas.
<p>(1) You could maintain your prose in a separate file, and then use inline comments of a specific format as a pseudo "cutpoint".
// :Some doco token: Insert common documentation here.
<p>Of couse, this would have to match the syntax of the file type. For xml it would be.. <!– …
<p>But what about source that is not yours …. ?
<p>(2) In your external documentation, you could use something similar to XPath to indicate where to apply the documentation. You could match accross packages, classes, methods, even use regular expressions to match various programming idioms.
<p><p> On compiling it, you could do some pretty cool stuff taking off from java2html. You could do popup divs liked little postit notes, or if you wantted to get facny, you could even figure out a way to do an overlay on top of the source.
<p>You may get stuck on line numbering, as an active project will render that obsolete in minutes.