The 'bundles' are now being built as pure OSGi bundles, rather than as Eclipse plugins under Tycho (with the associated problems). So it is now possible to simply deploy the bundles to Nexus using "mvn clean deploy".
The Eclipse plugins and update site are now built separately, by going to the 'tools' sub-folder and running:
mvn clean deploy -B -e -P helios-remote-target,\!helios
The Eclipse update site will include the OSGi bundles built using the first step.
I have just deployed to Nexus the latest 2.0.0-SNAPSHOT version - so any problems let me know. Atleast it won't be necessary to run a separate deploy.sh script now.