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For external files DLTK produce fake source module (it's not ExternalSourceModule). Since 5.9 it's related to correct IResource so parser, validation and outline works correctly. We should disable validation if SourceModule is inside ExternalProjectFragment.
New Gerrit change created: https://git.eclipse.org/r/125746
Gerrit change https://git.eclipse.org/r/125746 was merged to [master]. Commit: http://git.eclipse.org/c/pdt/org.eclipse.pdt.git/commit/?id=4e5456001e13b4b368216a68056547234effd9ae