Selfhosted
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Personally I have a secondary external SSD I use for my cache and transcode directories so that my transcodes aren't throttled by being read from and written to the same disk.
Also of note is that Jellyfin does have a cron job built into it to clear the transcodes directory. You can see it under Dashboard -> Scheduled Tasks -> Clean Transcode Directory. I have mine set to run every 24 hours.
Yeah, but the cleanup job doesn't seem to work reliably. I noticed because my home server ran out of disk space because the transcoding directory was over 30 GB in size.