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The break statement in the foreach loop should only be executed if $feGroups comtains at least one element. Otherwise the loop should continue until a group is found or the rootline ends.
If a file resource has a fe_group assigned but not any folder in the rootline, $feGroups will obviousely be empty before and after ArrayUtility::keepItemsInArray(). In such a case the fe_groups of the file resource have to be overtaken directly.
Take care of group inheritance? Imagine groups inside $feGroups are subgroups of other groups. So those other groups should also be granted access. So $feGroups should be enriched by these other groups. And this should be done for both - the $feGroups of the folder and for the file resource - before they are merged together with ArrayUtility::keepItemsInArray().
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Pull request for issue #244