As stated stupid me. Thanks for the clarification of my short sighted mistake.
Attached is a script that works great for our munkireport updates. Modify as needed:
#Commands Needed for MunkiReport upgrade (NOTE: Make sure to have the config set to update database : True;)
#!/bin/bash
#Remove old backup
rm -rf /Path/to/munkireport_backup/
#Copy old MR-PHP Folder to backup location
cp -r /Library/Server/Web/Data/Sites/Default/munkireport /Path/to/munkireport_backup/;
#Remove all files (Fresh Clean PHP app)
rm -rf /Library/Server/Web/Data/Sites/Default/munkireport;
#Clone current version from Github
#Copy old database and config into place
cp /Path/to/munkireport_backup/app/db/db.sqlite /Library/Server/Web/Data/Sites/Default/munkireport/app/db;
cp /Path/to/munkireport_backup/config.php /Library/Server/Web/Data/Sites/Default/munkireport;
#Establish permission rights ( ;P thanks to this article)
chown -R _www /Library/Server/Web/Data/Sites/Default/munkireport/app/db;
#Install the latest Munki Client
#Download the Install Plist to our Munki Repo Directory
I am typing this up from a half thought, feel free to adjust. I haven't had a full chance to test it yet, but this should remove the old backup, create a backup then download new munki report from github, followed by moving the config and database back in before giving the correct perms. I'll test it here in a little bit, but it looks good to me.