Ignore my cry for help, this was not a freenas or plex issue it was a permission issue, in windows I set everyone to have read access and the scan worked.
I was having the same problem. I fixed it by removing the Plex plugin on my FreeNAS box and installing Plex on my second Windows PC and pointing the library to the Windows media share I've been using for years on my FreeNAS box. Worked quickly and easily. Too bad it's this difficult to setup on FreeNAS. Really defeats the purpose of running it all on one box. Maybe somebody can post clear instructions on how to actually make it work.
Most of the time the issue is people putting the cart before the horse after they skip a step and blame it on FreeNAS. It has been pretty much the same since I started in 9.3 to set it up but they are used to a windows computer environment where pretty much everyone can read unless it's specifically set to not be accessible whereas FreeBSD is the opposite where no one can read unless that is granted. It works the same way in *nix environments around the world and a simple way to explain it is to send you here https://www.pluralsight.com/blog/it-ops/linux-file-permissions
When you create the storage to the plex-jail, say /mnt/Pool1/Films (top in the dialog screen) is the fysical path you have to map it to /mnt/Pool1/jails/plexmediaserver_1/var/db/plexdata/Plex Media Server/Media/Films (bottom) . So when you add "Films" in the Plex frontend and branch out for adding the directory it will show up the "Films".
Most of the time the issue is people putting the cart before the horse after they skip a step and blame it on FreeNAS. It has been pretty much the same since I started in 9.3 to set it up but they are used to a windows computer environment where pretty much everyone can read unless it's specifically set to not be accessible whereas FreeBSD is the opposite where no one can read unless that is granted. It works the same way in *nix environments around the world and a simple way to explain it is to send you here https://www.pluralsight.com/blog/it-ops/linux-file-permissions
His instructions are absolutely too much for someone who doesn't know CLI in unix. I've tried his instructions multiple times and I end up with a disaster of a file structure no matter what I do. As far as finding a video of how install plex, I've done it, and it worked once, now I can't get it to work again. I've gone as far as only using the root user and still nothing works.
Cannot believe how impossible this stuff is to get it to work.
There can't be permissions/users/groups conflicts because I only have one user. But still can't get anything to work the way people says it just does.
The one thing you do not realize is that there is a Plex user and group that is created when Plex is setup. So it is impossible to have a single user and group. Your SMB or NFS user may be one you created but even the default install of FreeBSD has multiple users.
So it's back to a simple permission error. If you have a hard time still and want to throw your hands in the air and give up feel free to pm someone and work out something to do it using teamviewer or something of that nature.
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