It would be useful then to separate out the doxygen and BoostBook files during the build stage so you can have a global reference while still having the BoostBook "user manual".
FWIW, I think this is the wrong way to go about things.
All of the information we need to generate an index (or multiple indexes) is in BoostBook, regardless of whether it comes from Doxygen or hand-coded BoostBook XML, and it's a small matter to actually generate the index once we've decided how it should look. Grouping documentation in different ways isn't hard either: we just need to decide what kind of flexibility we need and what the resulting DocBook (or even PDF/HTML) should look like.
Doug
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