Hi,
Coincidentally I've just created my first Share extension in a JAR yesterday, which also contains a client-side javascript file. It didn't work at once because I didn't use the correct url to the script file, because there's an extra /res/ in the path compared to when the files would be in the deployed WAR directory.
In short, files in META-INF in the JAR will be reachable at [host]:[port]/share/res/[filename].
I guess that means that if you want to change client reachable files, you'll have to change the files that reference them to point to copies in your JAR.
Regards,
Michael