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The documentation for "Perl Ignored Paths" is not clear - well to me anyway. I have a set of sub-dirs of the project-loc like dir/sub1, dir/sub2 etc that I would like to exclude. I tried adding the them like that ( dir/sub1 etc) but it didn't work.
Works for me. Maybe you forgot to Project > Clean afterwards to remove the error messages reported before changing the ignored paths preference.