Manually editing TV Show metadata file

[TheDreadPirate]

... all under their own subfolders ...

If you've got shows nested under an over arching folder, this will not work.  The only valid nested folders are seasons, extras, or specials.

https://jellyfin.org/docs/general/server/media/shows/

BAD
Shows > Star Trek > Star Trek TNG > Season## > s##e##.mkv
                           > Star Trek TOS > Season## > s##e##.mkv


Good
Shows > Star Trek TNG > Season## > s##e##.mkv
Shows > Star Trek TOS > Season## > s##e##.mkv

If you MUST organize it this way, you can use NFO files and Jellyfin will read those in and not use external metadata.

https://jellyfin.org/docs/general/server/metadata/nfo/