Develop a plugin which will be able to transform / invalidate other plugins in an installation. First iteration could be just a core with a hard-coded list of plugins / extension points which we want invalidated.
The goal here is to have all appropriate plugins in our installation, but disable the ones we do not want. Currently, JBDS removes the webtools jboss server-tools jar entirely, which makes the update site fail. What we need here is to have the webtools jboss server-tools jar IN hte installation, and loaded as a plugin, but have all of its extension points invalidated so it is effectively an empty non-contributing plugin.
org.eclipse.jst.server.generic.jboss_1.5.205.v200805140145 is the plugin we need invalidated. We need it's plugin.xml to be essentially empty with just base <plugin></plugin> tags.