I am going to hold off on this as I have run into an issue where bundles installed using and update site don't work with bundles installed using rpm if there is a bundle conflict between the two.
I am investigating.
After looking into this I realized that we cannot move forward with the reconciler solution.
The issue here is not the old issue of plugins not being installed properly using eclipse's installation system p2, but having plugins installed in two different locations each with it's own metadata. The first location being system directories used by rpm such as /usr/share/eclipse/ and the location used by the eclipse installation system ~/.eclipse. When there is a conflict between the two location eclipse simply picks the system installation resulting in the downloaded plugin and all downloaded plugins to be dropped.
We are working on a better solution for this problem.
Thanks, Sami