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Perspective configurations saves only views correctly. Toolbar and menu configuration is kind of playing game with rules you don't know. For example such steps: 1) Open 'Java' perspective. 2) Press Customize Perspective and uncheck File->Print in toolbar 3) Save it as 'Java2' 4) Open 'Java2' perspective 5) Press Customize Perspective. Customization for 'Java' perspective will be open. !ERROR! 6) Uncheck File->Save in toolbar. Now visually both 'Java' and 'Java2' haven't both File->Print and File->Save !ERROR! 7) Switch to 'Java' perspective 8) Press Customize Perspective. All subitems of File are checked. !ERROR! 9) Switch to 'Java2' perspective 10) Press Customize Perspective. Only File->Print is unchecked. !ERROR! The failing is not always the same, but this sequence must fail on some step. Something similar can be done for menu items. Also even not customizing something when you back from 'Debug' perspective to 'Java', debug toolbars are left sometimes and then not disappearing. General impression is that perspectives overwrite some parts of each other when saving. This bug is not new at all, noticed it like 7 years ago. Also this bug is related to #416295 and #407522, maybe some other.
Ivan, what build are you using? Eclipse for Java devs? Kepler SR1? PW
Right now eclipse-jee-kepler-SR1. However this bug appeared not in Kepler. I was using mostly jee builds.
This bug (or the biggest part of it) is a duplicate bug 404009 - saved perspective "shares" changes with the original one. Issues related to the "debug" toolbar are already fixed in 4.5 M5. Closing this one as duplicate. *** This bug has been marked as a duplicate of bug 404009 ***