Well all this sounds to me like PkgBase is not ready yet.One thing really scares me - a thing that I did not knew before - and its written in this comment:
- https://github.com/freebsd/pkg/issues/2485#issuecomment-3133396711
To quote:
So with PKGBASE the pkg delete -af command will WIPE almost all FreeBSD Base System including /rescue tools - so one will be left even without vi(1) (or any other) editor ...
That is far from POLA for my standards.
I would expect LOTS of misuses of pkg delete command with these defaults ... lots of guides on the Internet say 'just remove all the packages - its safe - you will still have your Base System' ... not sure if I have and good thoughts about these defaults ... but probably there is some logic behind these decisions that I just do not understand ...
So for now - with PKGBASE - start to remember this one single rule - never use pkg delete -af command ...
It has been 9 years and it amazes me that no one has thought of what would happen if you ran pkg delete -af.
It's good to see that at least it doesn't force you to update your base while updating 3rd party packages ... .
If they actually want to design it well it should have it's utility, database, caches, folders and ... isolated away from the 3rd party pkg stuff so that nothing from one side can effect the other.
But it seams like after 9 years PkgBase is still basically the Linux method of slapping vital system packages in the same package
manager that manages 3rd party software and the fun part is that it is gonna get forced on us in few months.
It would be fun to see the horror stories though ... .