I tend to use wikis for this sort of thing ... which admittedly may be the worst solution of all, except for all the others that have been tried so far. :)
From my limited googling on this topic, I get the feeling that this is a hard problem. At least, I couldn't find an example of an unqualified success story in this domain. For example, this post indicates that AnnoCPAN has hardly been an unqualified success. If anyone knows of a "successful" version of a similar concept to AnnoCPAN, please let us know.
References
In reply to Re^3: Tools for annotating module code?
by eyepopslikeamosquito
in thread Tools for annotating module code?
by nysus
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