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This is due to mainProjectHack we use to determine the main project. Right now this misbehaves e.g. when opening the first project, when, before the project finishes loading, the dialog to select main project is dispayed. We need to figure out how to find out the main project without disturbing the user.
Fixed in M9 by using the new 5.0 API to obtain main project, avoiding the hack that caused problems
Verification of old issues.
Closing old issues.