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1. Create new local repo. 2. Import repo as project. The .project file is always shown with a "shared" decorator, and the staging view is empty. Only explicit refresh of the staging view changes the decoration to "question mark" and lists the file as new staging entry.
Related to bug 553064?
No idea, didn't debug into that yet. Just happened to create a bunch of repositories today for Jenkins pipelines and saw the error with each of them. With just one repo and that effect I might have assumed an error on my side...