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I think pdfparanoia should inject metadata into each pdf it scrubs. This data will be a json blob that contains information like which version of pdfparanoia was used to scrub the file, what time the scrubbing occurred, previous scrubbing history, etc.
Scrubbing history should record which objects were removed from the document. Eventually this might be useful for debugging what happened to a pdf in a collection.
Also, this could be an interesting hook for storing metadata about a paper inside the paper itself. There could be a json blob-- like the data returned from zotero translation-server and zotero translators-- that gets added by pdfparanoia next to the scrubbing history.