You'll have to write a perl script. Take no notice of the nay-sayers above.
Such a tool could work with libraries that are designed to only make function calls explicitly. That means no delegates or pointers to functions would be allowed, the use of which in any case only results in unreadable "spaghetti code" and is not best practice. Even if it removes some of these hidden functions you'll discover most if not all of them in testing. The ones you dont discover will be so infrequently used that they will not be worth your time fixing them. Dont obsess with perfection. People go mad doing that.
So applying this one restriction to JavaScript (and libraries) will result in incredible reductions in page size and therefore load times, not to mention readability and maintainability. This is already the case for tools that remove unused CSS such as grunt_CSS and unCSS (see http://addyosmani.com/blog/removing-unused-css/) and which report typical reductions down to one tenth the original size.
Its a win/win situation.
Its noteworthy that all interpreters must address this issue of how to manage self modifying code. For the life of me I dont understand why people want to persist with unrestrained freedom. As noted by Triptych above Javascript functions can be called in ways that are literally "insane". This insane fexibility corrupts the fundamental doctrine of separation of code and data, enables real-time code injection, and invalidates any attempt to maintain code integrity. The result is always unreadable code that is impossible to debug and the side effect to JavaScript - removing the ability to run automatic code pre-optimisation and validation - is much much worse than any possible benefit.
AND - you'd have to feel pretty insecure about your work to want to deliberately obsficate it from both your collegues and yourself. Browser clients that do work extremely well take the "less is more" approach and the best example I've seeen to date is Microsoft Office combination of Access Web Forms paired with SharePoint Access Servcies. The productivity of having a ubiquitous heavy tightly managed runtime interpreter client and its server side clone is absolutely phenomenal.
The future of JavaScript self modifying code technologies therfore is bringing them back into line to respect the...
KISS principle of code and data: Keep It Seperate, Stupid.