In WTP, server adapters own the publishing logic (which includes getting
the app ready for publishing). There is a publish steps extension
point that lets you add additional logic to the publish operation, but
there is no way to completely replace the packaging. That wouldn't work
anyway, since different server adapters have different requirements for
the form that the app must be in for publishing. Some require a WAR
archive, some require an exploded WAR directory, and some have
proprietary descriptors that tell the server where to find pieces of the
WAR without actually physically assembling it.