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output : ./docs/jquery/core.js
Take a look at #49 and see if it works for your use case
npm install -fg https://github.com/nevir/docco/tarball/recursive_dirs if you want to try it out, npm install -fg docco to revert to the official
npm install -fg https://github.com/nevir/docco/tarball/recursive_dirs
npm install -fg docco
Related to pulls #45 and #49. However they both handle this in different ways.
These are feature requests and not as important and easy to review as bug fix pulls, so take @nevir's suggestion and try them out for yourself in the interim.
I'm afraid I don't understand what the problem is here ... Please feel free to try the latest version of docco, and write back if you're having trouble.