I installed wordpress with apt, which ties in a lot of directories, so I suspect that using the built-in core update tool will break the installation; but wordfence constantly demands that I update using said tool -- which is probably much more up-to-date than the linux distro repository. Do I have to wipe it out and start over in order to resolve this annoying bind?
Do I have to wipe it out and start over in order to resolve this annoying bind?
No, since WordPress is not system level software, you can copy it, and its data elsewhere, or migrate it to a new instance installed using more standard means. You do not need to install and rebuild your site from scratch.
To get around WordFence however, you will need to update WordPress to the latest version as it wants, and do it using apt and only apt if you want to continue to use that tool. At the time of writing, that would be WordPress 5.7.2 with 5.8 due imminently. If you do this any method other than apt then the changes will be undone when apt next processes that package for an update, or a forced reinstall.
If your repository does not provide the current latest then you should contact them immediately, v5.3.2 has known security issues ( at the time of writing 5.3.8 is the newest version of the 5.3.x branch with hotfixes )
I actually like the idea of updating wordpress via apt, as if it is done correctly it can eliminate some headache with installing and configuring the DB and web server while followinf best practice, but the question is how reliable it is to help you maintain wordpress up to date. from looking at https://packages.ubuntu.com/groovy/wordpress it seems that ubuntu LTS is stuck with wordpress 5.3.2, so a potential problem is that you will upgrade wordpress via the wordpress admin or wp-cli and one day when you will run apt update you will cause wordpress to actually be downgraded.
So if you go the apt way, you should probably commit yourself to keep using apt which might actually be OK in some specific settings.
As for wordfence.... with all due respect to them, wordpress setups can vary alot. I would use their "error" indications as a trigger to reevaluate what I am doing, but not as a bible.
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