It downloads in /var/lib/transmission/Downloads but i want them to download in /mnt/Jellyfin/TV Shows/ so i can watch and keep seeding them
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You don’t want to download to JellyFin/TV. Keep the downloads in the original location and make sure hardlinking is enabled, the file will appear in both locations so you can watch and seed at the same time.
https://trash-guides.info/Hardlinks/Hardlinks-and-Instant-Moves/