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If you open the Debug perspective and then close it the Package Explorer disappears. Root cause was that I opened the second perspective using the perspective switcher which performed the operation 'locally' rather than going through the WorkbenchPage#setPerspective code. This meant that the 'openPerspectives' list wasn't updated which meant that the 'closePerspective' call delegated to 'closeAllPerspectives' since it thought there was only one open.
Created attachment 173028 [details] Patch to have the perspective switcher use the WorkbenchPage to close
Oleg, to get the NPE start with a clean WS, open the Debug perspective and then close it.
Created attachment 173031 [details] Patch for the injection problem The patch limits the listeners receiving UNINJECT event to the listeners created from injection, skipping pure #runAndTrack entries. (After looking at the code, the code doing uninjection processing needs a cleanup. I'll open a separate bug for that, but it is likely to be done after 4.0, unless there turns out to be more issues in it.)
Created attachment 173036 [details] Patch that allows perspectives to be closed/reset
Committed in >20100629. Applied the patch (without the changes to the PRE which were checked in under bug 317591).