Automatically building Eclipse plug-ins has been sort of difficult for quite a while.
Running the build manually from PDE works, but it’s pretty much a black box and you can’t always get what you want from that. It can sign plug-ins when choosing Export… -> Deployable plug-ins…, but it can’t do this when building a whole update site. If you are used to Maven, Ant or another command line build tool, then things like this are truly annoying.
There are, of course, some tools provided by the Eclipse Foundation for headless building of plug-ins, but they don’t seem easy to set up or convenient to use. Tycho for Maven 3 aims to change that, making it possible to build OSGi bundles / Eclipse plug-ins in an environment familiar to most developers and with minimal additional configuration.