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Feb 20, 2017 at 20:36 comment added Majid Alfifi Thanks for the term "shadowing". I have updated the question for future readers.
Feb 20, 2017 at 19:47 comment added Kevin I have heard of this as "shadowing" a directory. It is often done on purpose when mounting volumes within containers. I am not aware of a program that would have detected this, unless there is a special flag for it in du. Maybe re-word the question in order to attract people that may know a way of discovering the issue sooner, or who know of a method of detecting shadowed directories more readily.
Feb 18, 2017 at 3:11 history answered Majid Alfifi CC BY-SA 3.0