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Produce id attributes for all entities generated by Doxygen. For refs, generate link tags referencing those ids. Preface the ids with "doxygen." prefix to avoid potential clashes with ids that may be present in other places of the resulting DocBook document. Also add the document refid to the prefix to avoid potential clashes between multiple Doxygen-generated documents with SHORT_NAMES=YES. In order to pass through the generated ids without modification (to keep links working in the output), change generate.id template so that it returns the value of the id attribute, if one is present, instead of generating a new id. The end result is that all references generated by Doxygen (to methods, classes, variables and so on) propagate to the final HTML output instead of being stripped during Doxygen to BoostBook translation.