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Shoko is the only nonstandard plugin I use.
I haven't heard of Shoko. How is it different from metadata grabbers like AniDB and AniList? The website makes it seem like it just uses AniDB to tag your episodes and series.
It organizes and renames files and also syncs your watch statuses for shows. Basically it works as a complete library management tool. It also checks the file hashes for anime against AniDB, so it's more reliable at getting the metadata right.
I use Sonarr to handle naming so I'd imagine this wouldn't play nicely with it right?
I struggled for a long time to find a way to have One Piece to show in Jellyfin with the absolute episode numbers, and even though I found a way it wasn't worth the tradeoff for me. I now just deal with TVDB organizing (S22E37 which is actually E1122 for instance) and just be at peace with it.