I just upgraded, and while it mostly has gone well, I do have a problem with where things are mounted. While volume1 is mounted on /mnt/volume1, there is also a /mnt/mnt/volume1, which is less than desirable as nothing is now in it's proper place. 
I'd appreciate some help, I'm hoping it's as simple as changing my altroot to something else.
Code:
freenas% mount | grep -E 'volume1 |tmpfs on /mnt'
tmpfs on /mnt (tmpfs, local)
volume1 on /mnt/mnt/volume1 (zfs, local, nfsv4acls)
freenas% zpool get altroot volume1
NAME     PROPERTY  VALUE    SOURCE
volume1  altroot   /mnt     local
freenas%
For example, ssh myuser, to the machine.
Code:
Welcome To FreeNAS
Could not chdir to home directory /mnt/volume1/datashare/myuser: No such file or directory
freenas% echo $HOME
/mnt/volume1/datashare/myuser
freenas% zfs list | grep myuser
volume1/datashare/myuser                                        3.19T  3.09T     2.34T  /mnt/mnt/volume1/datashare/myuser
volume1/datashare/myuser/DVR                                    47.3G  3.09T     47.3G  /mnt/iocage/jails/channels-dvr/root/media/DVR
freenas% zpool get all volume1 | grep altroot
volume1  altroot                        /mnt                           local
freenas% zfs get mountpoint /mnt/mnt/volume1/datashare/myuser
NAME                       PROPERTY    VALUE                               SOURCE
volume1/datashare/tcovert  mountpoint  /mnt/mnt/volume1/datashare/tcovert  inherited from volume1
freenas%
Additonally, all of my jails are down as well, as they can't find their baseroot.
Code:
freenas% iocage list
You need to be root to convert the configurations to the new format!
You need to be root to convert the configurations to the new format!
+------+--------------+---------+--------------+------+
| JID  |     NAME     |  STATE  |   RELEASE    | IP4  |
+======+==============+=========+==============+======+
| None | ansible      | down    | 11.4-RELEASE | DHCP |
+------+--------------+---------+--------------+------+
| None | channels-dvr | CORRUPT | N/A          | N/A  |
+------+--------------+---------+--------------+------+
| None | git_jail     | down    | 11.4-RELEASE | DHCP |
+------+--------------+---------+--------------+------+
| None | gitlab       | CORRUPT | N/A          | N/A  |
+------+--------------+---------+--------------+------+
| None | plex         | down    | 11.4-RELEASE | DHCP |
+------+--------------+---------+--------------+------+
| None | prometheus   | down    | 11.4-RELEASE | DHCP |
+------+--------------+---------+--------------+------+
| None | remotelog    | down    | 11.4-RELEASE | DHCP |
+------+--------------+---------+--------------+------+
freenas% zfs list volume1/iocage
NAME             USED  AVAIL     REFER  MOUNTPOINT
volume1/iocage  26.4G  3.09T     15.6M  /mnt/mnt/volume1/iocage
freenas% zfs get mountpoint volume1/iocage
NAME            PROPERTY    VALUE                    SOURCE
volume1/iocage  mountpoint  /mnt/mnt/volume1/iocage  inherited from volume1
freenas%
And, what /mnt looks like, well, a selection so as to not spam everyone.
Code:
freenas% find /mnt -maxdepth 4                                                                                                                                                                           
/mnt                                                                                                                                                                                                     
/mnt/volume1                                                                                                                                                                                             
/mnt/volume1/jails                                                                                                                                                                                       
/mnt/volume1/jails/.warden-template-pluginjail-10.3-x64                                                                                                                                                 
/mnt/volume1/jails/.warden-template-pluginjail-10.3-x64/libexec                                                                                                                                         
/mnt/volume1/jails/.warden-template-pluginjail-10.3-x64/rescue 
/mnt/iocage
/mnt/iocage/jails
/mnt/iocage/jails/channels-dvr
/mnt/iocage/jails/channels-dvr/root
/mnt/md_size
/mnt/mnt
/mnt/mnt/volume1
/mnt/mnt/volume1/.freenas
/mnt/mnt/volume1/.freenas/gui-install-environment.tar
/mnt/mnt/volume1/.freenas/pre-install
/mnt/mnt/volume1/.freenas/tmp
/mnt/mnt/volume1/.freenas/lib
/mnt/mnt/volume1/.freenas/etc
/mnt/mnt/volume1/.freenas/install
/mnt/mnt/volume1/.freenas/firmware.img
/mnt/mnt/volume1/.freenas/bin
/mnt/mnt/volume1/.freenas/gui-boot.tar
/mnt/mnt/volume1/.freenas/gui-packages.tar
/mnt/mnt/volume1/jails
/mnt/mnt/volume1/jails/git_jail_orig
/mnt/mnt/volume1/jails/.warden-template-pluginjail-9.3-x64
/mnt/mnt/volume1/jails/.warden-template-standard-11.0-x64
/mnt/mnt/volume1/jails/plex
/mnt/mnt/volume1/jails/.git_jail.meta
/mnt/mnt/volume1/jails/.warden-template-pluginjail-9.2-x64
/mnt/mnt/volume1/jails/.warden-template-pluginjail-10.3-x64
/mnt/mnt/volume1/jails/.plex.meta
/mnt/mnt/volume1/jails/.warden-files-cache
/mnt/mnt/volume1/jails/.redmine.meta
/mnt/mnt/volume1/jails/redmine
/mnt/mnt/volume1/jails/.warden-template-standard-11.0-x64-20180819223447
/mnt/mnt/volume1/jails/.warden-template-standard--x64
/mnt/mnt/volume1/jails/.plugins
/mnt/mnt/volume1/jails/.warden-template-standard-10.3-x64
/mnt/mnt/volume1/datashare
/mnt/mnt/volume1/myuser
/mnt/mnt/volume1/timecapsule
/mnt/mnt/volume1/timecapsule/.AppleDB
/mnt/mnt/volume1/timecapsule/backup_myuser
/mnt/mnt/volume1/plexdata
/mnt/mnt/volume1/plexdata/Plex Media Server
/mnt/mnt/volume1/plexdata/Plex
/mnt/mnt/volume1/iocage
/mnt/mnt/volume1/iocage/.plugins
/mnt/mnt/volume1/iocage/images
/mnt/mnt/volume1/iocage/defaults.json
/mnt/mnt/volume1/iocage/default_rc.conf
/mnt/mnt/volume1/iocage/jails
/mnt/mnt/volume1/iocage/log
/mnt/mnt/volume1/iocage/download
/mnt/mnt/volume1/iocage/templates
/mnt/mnt/volume1/iocage/releases
/mnt/mnt/volume1/iocage/defaults_backup.json
freenas%