Even on a pkgbase system, it should be possible to use freebsd-update -j
to upgrade a non-pkgbase jail, at least for the team being. However,
the check_pkgbase() call came before get_params, so BASEDIR was set to /.

Make check_pkgbase() a pure function and call it after get_params().
While here, use pkg -r ${BASEDIR} instead of pkg -c ${BASEDIR} since the
latter requires root privileges. freebsd-update is supposed to be run
as root, but it doesn't actually check this that I can see, so let's not
make that assumption here since it affects the result of the function
(i.e., pkg -c ${BASEDIR} always fails as a non-root user).