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Newly created projects should be added to the currently active working set. The current behaviour of popping up a dialog asking if the working set should be deactivated is not good. By analogy with: 191512: Newly created queries/categories should be added to the currently active working set https://bugs.eclipse.org/bugs/show_bug.cgi?id=191512 Note that this means projects explicity created using "new project" as opposed to projects created on the file system.
Most dialog pages for creating projects (e.g. for Java projects) have controls for selecting task working sets to add new projects to. Automatically adding the project to all active working sets would break the explicit control of the user. I can see how an option to add projects to the Window Working Set would be helpful though and you could consider filing a bug against JDT/platform to request that.
Those working set lists are empty for me - task working sets do not show up there...
Yes, that's a limitation of the platform.