Flag or mark in a certain way a file in the content collection if this is link from the course. The idea is to easily identify files that are not being used in the course and be able to delete duplicated files or content is not being use at all.
I think Bb Ally marks the files that are scanned for accessibility but from the content collection only the files that are linked in the course are checked for accessibility. So maybe the same sort of logic can be use to indicate whether or not a file is linked in the course. Indicate it with a link icon or something similar.
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