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Last time I looked at Paperless-NGX it insisted on taking the source files and moving/renaming them so it could manage them itself. In fact IIRC the only way to add files was to give them to the app (or upload via web UI) so it could take them over.
Does it still do that?
I don't like tools that demand to take over the original files. I'd prefer it if it could watch a read-only folder for new files. Immich for example or Jellyfin can do that.
You can define the folder structure used by the app, so if needed, you can backup your documents as raw files (of course, you'll lose metadata from Paperless).
Yeah it maintains it's own folder structure and I'm not aware of a way past that (not that I looked).
There's several more options to get the documents into it though. Ingest folder, via email, certainly more.