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If a resource is disabled from validation and then removed, a NPE will be triggered the next time a resource is enabled or disabled. It most likely occurs because IContainer#findMember() can return a null, and that return result is stored in the disabled list regardless in org.eclipse.wst.validation.internal.DisabledResourceManager#load(IProject) line 91.
Created attachment 226139 [details] proposed patch, stores paths instead of handles in disabled set
I like this patch.. Carl, Rosendo can you take a look?
Looks good. Reviewed.
Pushed to master and released v201301291945.
*** Bug 424407 has been marked as a duplicate of this bug. ***