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On Package Explorer there is a auto-managed working set called "Other Projects" which gets all projects which aren't in any working set. Project Explorer does not show it. This is a big problem if you are working with working sets as top level elements, because if you create a new web/c/c++ project it initially falls into no working set, and does not show up in project explorer.
*** Bug 229537 has been marked as a duplicate of this bug. ***
*** This bug has been marked as a duplicate of bug 266030 ***