Here are some links that might lead you where you want to go:

There are more out there, but not yet a lot. The key here is to combine your search on XML with a search on Literate Programming. Because that is pretty much what you describe- literate programming that is. In fact, excepting the small matter of coding (SMOC tm), you not only should get every thing on your list (index, master table ofcontents, etc.), but you also get your source code out of the same black box. If you extend your schema, you also get a cross reference for all parameters used and if you want, all variables cross referenced with scoping information etc. Point of fact, if you tag it, you can manipulate it! Again, this is what LP is all about.

Having said that, there are two problems that come to mind. The first problem is that most of the magic involved around LP typically revolves around translating some initial form into LaTeX, and you've already indicated that, that wouldn't be desirable. Second problem, is tied to XML. While the idea of LP is comparative old (20 years comes to mind), expressing this in XML is pretty much a new thing. New enough that there aren't a lot of ready made tools that spring to mind. Most of them have been mentioned already in either this thread or the earlier one.

All of that leads me to this:

I've given this topic quite some thought, since it is pretty much what I'm getting paid for at the moment! I've looked at virtually every solution to this problem out there, where 'looked at' means actually tried. To be truthful, I haven't found a single solution yet. Which same implies that I'm currently leaning in the direction of 'roll your own'. My general idea is to write a filter that uses a hybrid approach, i.e. part XML, part LP, part target language (Perl at the moment) to generate source, reference and help documents in html, and pdf. And of course, I'd write this in Perl- as a module, in the usual form of a 'something' 2 'something' app (pod2html, pod2pdf, and similar).

To grok the LP thing here is the single best pointer that I know:

hsm

In reply to Re: XML documentation formatting and transformations by hsmyers
in thread XML documentation formatting and transformations by John M. Dlugosz

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