My idea would be to have a sort of a hyperlink/anchor for each such cross-threaded flag/variable, which would link to a document on the flag/variable or a part of the sources relevant to it (in my case, the declaration); for backward compatibility again as some special form of the comment. The editor can then maintain a collection of anchors related to a particular variable and offer it immediately together with the "document" e.g. in a separate window upon clicking on the variable name; no hassle with multi-file searching. It can have also impact on the resulting documentation, of course; the details could be worked out.