Do you really want to let your
customers update the WAR file themselves? I don't know if that is a good idea... (assuming they are not
Java developers). What if they do something wrong so that your software doesn't work anymore?
If there are resources that they have to be able to change themselves, then you could store them somewhere else, not inside the WAR file. Then they'd just have to put the right files in a directory somewhere and your webapp will pick them up from there.
What exactly are the replaceable parts of your application? Just data files (HTML pages, images, ...) or runnable code?