You have a few options...
1) You can disable the building of specific packages in JBossIDE's packaging configuration by checking/unchecking the check-box next to the package you want do enable/disable. It might turn out to be a pain, but you would need to disable the WAR build, Run Packaging, sign your jar, go back and re-enable the WAR build, and Run Packaging again.
2) If your packaging configuration is relatively stable (i.e. you won't need to change it very often) it might be easiest to copy the packaging-build.xml to a new ant script, and editing it manually so that after the client.jar is built you can digitally sign it via ant. Then instead of using "Run Packaging" you can just run that ant script.