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Am I the only one here successfully using Sonarr to take care of Anime? Sonarr has the ability to sort by absolute/relative episode you just need a profile for it.
If I really need to bother with any renaming, I'll use "RenameMyTVSeries" to mass-rename things, and drop them in the folder where Sonarr wants; or usually just have Sonarr grab the anime itself and apply its renaming rules.
Jellyfin is going to want:
Grouping seasons into a series folder doesn't work well in some cases, because that's not the way they are released in Japan. A new season is (most of the time) effectively an entire new show entry. Show seasons are mostly a north american thing. No matter which software you use, there's always going to be some minor issues if you group seasons into one entry.
In instances like this, you simply use a single Season 1 folder, with absolute naming for episodes. It's really that simple.