Hi David,
Referring to #27 I think too, that the design of the extension should be rethought. As a first suggestion I'd like to propose to switch to a JS parser to identify functions (and possibly other things to annotate) instead of using regular expressions.
Codemirror uses acorn.js anyway for code completion, so why not use it too to generate the jsdocs? What's you opinion on that?
As a start I wrote my first brackets plugin from scratch which uses acorn.js and can be found at:
https://github.com/Hopiu/brackets-annotate-extension
(Of course I won't publish the plugin in the extension repo)