If you're using the WTP-type projects, I haven't investigated this specific case yet, and can add it to my to-do list.
If on the other hand you're using regular projects and the "Project Archives" feature, then yes. You can create your project, all your code, etc, open the Project Archives view, create your archives, and set it to automatically build the archives whenever a build is initiated, and then also automatically publish to a list of servers at the same time.
Once you do this set-up, you can turn auto-build off, make some changes, observe that the archives aren't rebuilt nor published, then do a ctrl+b, and observe that your bin folder changes, your archives change, and the deploy is also changed.
I'm using whatever sort of project JBDS creates when a new Seam project is generatied. AFAIK this is a WTP-style project. So consider this a nice-to-have. Should I file a JIRA?
Yes file a JIRA.
I'll have to patch upstream to fix it, I think, but this sounds like a pretty good idea. I'll try to talk to Angel about it ASAP.