As per the discussion on sbt list we found that sbt exclude is the equivalent of Ivy's <exclude org="org.atmosphere" module="atmosphere-compat-jetty" type="jar"/>. Unfortunately this means that when we try to exclude a transient dependency which is a bundle:

"org.vaadin" % "dontpush-addon-ozonelayer" % "0.4.6" exclude("org.atmosphere", "atmosphere-compat-jetty")

atomsphere-compat-jetty it is not excluded. The workaround is to use Ivy directly:

ivyXML :=
  <dependency org="org.vaadin" name="dontpush-addon-ozonelayer" rev="0.4.6">
      <exclude org="org.atmosphere" module="atmosphere-compat-jetty"/>
  </dependency>

Mark noted in the thread I linked to above that this is a bug and could be fixed for 0.12. Hopefully that can be done.

Thanks!
Chris.