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Fix test collection from packages mixed with directories. #3768 and #3789 #3802
This should fix the issue but I still can't find a better fix. See the comment in the code.
What happens is: the files and directories are marked as duplicates when the Session starts collection even though they're not turned into nodes right away (the package nodes will do that later). Ideally is that when Session finds a Package it should stop recursing and move on.