Do not attempt to upgrade packages in the rootfs chroot when running
"pmbootstrap install".
This was responsible for placing every single package in /etc/apk/world
(which should only hold the packages explicitly installed), because the
upgrade function was literally implemented as getting a list of
installed packages and explicitly running pmb.chroot.apk.install on each
of them. The intention was to rebuild these packages if they were outdated,
I guess I didn't realize that this makes /etc/apk/world unusable when I
introduced this three years ago in 51bdc243 ("Properly rebuild/install
packages when something changed").
Remove pmb.chroot.apk.upgrade altogether, because:
1) pmb.install.install builds and upgrades outdated pmaports
2) pmb.install.install is the only user of pmb.chroot.apk.upgrade
3) 'pmbootstrap init' is warning that the chroots do not get upgraded
automatically, so let's not go against that expectation. users who
want an updated rootfs chroot can simply run zap and install again.
Replace it with a call to pmb.helpers.repo.update, because we still need
to update the APKINDEX files before attempting to build/install the
generated list of packages.