Hi @nathanRona sorry you are having such a torrid time getting Mango to upgrade. It seems that the issue is that you have started Mango directly using supervisorctl to launch the java process. Unfortunately this means that Mango cannot upgrade itself. It is the script that launches Mango (ma.sh -> ma-start.sh -> java) that does the unzipping of the new core upgrade file.
I recently created a new script (start-mango.sh) for starting Mango as the old ones were a bit fragile. This script is our new preferred way of launching Mango, we left the old ones so upgraded systems did not break.
I updated the help documentation here - https://help.infiniteautomation.com/linux-installation
What Linux distribution are you using? Does it use systemd?