We are pulling MediaWiki from the official git repository via these instructions. Similarly, themes and extensions are also pulled from official MediaWiki repositories as are extensions available in this format.
Since I know this system works, there is no sense in re-hashing how to install from scratch.
What is confusing, however, is upgrading, especially when you google "upgrade mediawiki" and come up with this mess of instructions. Hence, here is a boiled down version of what I do to upgrade the Fairy Garden Wiki so that I don't have to remind myself each time.
sudo git pull- This sometimes requires a merge of locally edited files, but is otherwise straightforward. This SHOULD also merge in with a local copy that is "ahead of the remote" so long as it is largely unedited.
sudo -u www-data composer update --no-dev- They decided to start using composer to manage third-party (vendor) plugins. I'm fine with this, so long as I don't need to think. I always forget to not run composer as root, so make sure this command is more or less run as-is.
sudo php maintenance/update.php- This is the part that updates the database. When I tried running just now (2019-01-09), it initially did not work because the composer dependencies had not been updated first.
cd extensions/<extension directory>/; sudo git pull;- For each git-supported extension, just run a git pull.
cd skins/<skin directory>/; sudo git pull;- For each git-supported skin, also just run a git pull.
And that's it!!