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We set various VM arguments in eclipse.ini: -Dorg.eclipse.equinox.simpleconfigurator.useReference=true -Dorg.eclipse.update.reconcile=false -Dorg.eclipse.p2.update.compatibility=false If these properties are missing when self-hosting with p2, things are horribly broken. Simple configurator doesn't use reference URLs, so all bundles are copied by the framework on startup. If automatic updates downloads new plugins, update.configurator attempts to install them and the IDE blows up because it is not dynamic. In short, these properties are absolutely critical. I spent several hours this week trying to figure out why things were breaking for me, because I had added a VM argument on the command line last week for doing YourKit profiling. Perhaps these arguments should be added in config.ini instead of eclipse.ini so they won't get lost if vm arguments are added on the command line.
On Andrew's suggestion I have created a setProgramProperty command who causes the property to be written in the config.ini. This is released in HEAD.