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When you delete your Activator class, when you delete an exported package etc., MANIFEST.MF isn't updated. When you delete a resource that is included in build.properties, the file isn't updated. PDE should implement a DeleteParticipant to deal with refactorings implied by resource deletion.
good call! Oh boy, people are getting spoiled by PDE and your work Benjamin ;)
We will look at this in 3.5
*** Bug 127169 has been marked as a duplicate of this bug. ***
*** Bug 173064 has been marked as a duplicate of this bug. ***
Note that bug 127169 was about deleting something *inside* a plugin.xml, so a DeleteParticipant will probably not catch it if a user deletes an extension point in a plugin.xml. Builders like PDE's Plug-in Manifest Builder are typically not implemented as refactoring participants, since participants are only notified of explicit refactoring actions. You should rather implement a resource change listener (and maybe a Java model listener) to implement incremental builds correctly.
Not planned for 3.5
This bug hasn't had any activity in quite some time. Maybe the problem got resolved, was a duplicate of something else, or became less pressing for some reason - or maybe it's still relevant but just hasn't been looked at yet. If you have further information on the current state of the bug, please add it. The information can be, for example, that the problem still occurs, that you still want the feature, that more information is needed, or that the bug is (for whatever reason) no longer relevant.
Please remove the stalebug flag, if this issue is still relevant and can be reproduced on the latest release.