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I don't have a solution for you, but I will be watching this thread. Currently, I use Sonarr for library organization, but it doesn't always work well with anime due to title differences and differences between how seasons/specials are numbered in different databases. So, Shoko was on my radar to try out at some point since it uses anidb.
I've read that Shoko works for many people, but yeah... I must be doing something wrong. Right now I'm manually renaming everything to the recommended Jellyfin naming structure and using the AniDB or Anilist plugin in Jellyfin to get the rest of the metadata. A bit of a pain... If I get no responses, maybe I'll look into Sonarr or Tiny mediamanager