What he means is, instead of having a file you name

    myscript.js

you name it

    myscript-[sha1 hash of contents].js

and you set its cache header to expire at some improbably point in the far far future. If you should happen to update the contents of your script file- the sha1 hash will change, and thus its name and its cache entry will also change, in lockstep with its contents. The only fiddly part of this approach is you must also update all references to the new version of the file. If you're clever you can automate this with templates and build systems.

What this guarantees is that if your index.html and app cache manifest refer to myscript-[some specific sha1], you're guaranteed that the contents of the script are consistent with what that index.html file expects there.