Javascript documentation tools are still relatively immature, so there aren't 50+ ones like there are for say JavaDoc, and the ones that do exist don't handle complex cases like jQuery plug-ins (or at least none of the ones I've ever seen).
However, Javascript is an extremely flexible language, so you could just rewrite your plug-ins in a way that makes your documentation tool happy.
For instance, instead of:
(function($) {
$.yourMethod = function() {/* do something */}
})(jQuery);
you could do:
function yourMethod = function() {
/* do something */
}
(function($) {
$.yourMethod = yourMethod;
})(jQuery);
delete yourMethod
or just:
jQuery.yourMethod = function() {
/* do something */
}
Those two options aren't truly identical; the first one will overwrite any existing yourMethod function, and the latter will not have the nice "privacy" of the standard plug-in format. Depending on what you're writing this plug-in for, those issues may or may not matter to you.
If they don't, re-styling your code may be a viable way of making your JSDoc parsable. If not ... good luck finding a mature enough JSDoc tool (or writing your own) :-)
