Indexing intrinsic metadata in a deposit using a sub-folder for the content

In a deposit, the root directory contains a sub-directory with all files. I believe that the content of the real root directory isn't indexed (due to the fact the indexer indexes only the root directory targeted by the revision)

We are trying to get researchers to add codemeta.json files and these should be indexed even if they are in a sub-directory.

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Migrated from T2472 (view on Phabricator)