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[news.eclipse.platform.rcp] CommonNavigator on blank workspace

I've gotten org.eclipse.ui.navigator.CommonNavigator to work on my workspace (backed by regular filesystem) following a couple of exmamples online (http://www.cpuidle.de/blog/?attachment_id=50, link down as of writing).

However I'm observing some quirks with this navigator; one of them is regarding starting it with a blank workspace... note that the workspace is blank in the sense that it's a purely blank folder without .metadata (this should be the initial status when the rcp app start for the first time); now the issue is that whatever change I did to the workspace is not reflected in the navigator (while "Project Explorer" works because it's not based on CommonNavigator). But once I shut down the app and restart it, everything works fine. I've tried a couple of times and now I have verified that as long as you have a .metadata folder created, all the changes will be reflected in the navigator; even if the workspace contains no projects at all(just a ".metadata" folder with data created automatically).

Has anyone observed the same behavior? Or am I missing something?

Thanks,
Guang