As we proceed with the issues in #1448, and add more features to file entities, it seems like the expectations around how files are cleaned up by the system will change, and if we allow site-wide settings for garbage collection in #2896, we should also look at settings on a per-file-entity basis.
We currently have a flag in the database to mark whether files in the database are permanent, which excludes files from being deleted during garbage collection. I believe that this is checked if a file is uploaded outside of the context of a node field.
We might want to expose that flag to users, so that when they are adding/editing a file entity, they can mark whether a file should be excluded from garbage collection if it is no longer being used.
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