You can't assign a certificate to a WAR. Certs are applied to the server as a whole, not an individual webapp or even virtual host (which can be a real pain).
Thus, you have to create a discrete certificate file for the server machine that it will be deployed on (since certs both aid in encryption and certify that you're really talking to the indicated host machine).
I'm afraid that SSL configuration is not considered as part of the
J2EE spec, so there's no J2EE support for that. You have to do it manually. Or, failing that, do what I do and make an OS installer package for the cert and its containing keystore (MSI, RPM, deb, pkg or whatever, depending on the OS).