pkgbase: don't remove the 'latest' symlink until the repo is final

We can encounter many issues in the pkg-repo(8) process which would
currently leave us with no more 'latest' symlink in the repository. The
main problems with this are that we've now broken a subsequent
update-packages because we can't determine a PKG_VERSION_FROM, but
also we break configured clients that are still expecting to see *some*
repository.

Switch to just replacing the latest symlink entirely after we have
made it past the pkg-repo(8) step so that we only swap over when we have
a finished repository.

Reviewed by: bapt, emaste
MFC after: 3 days
Differential Revision: https://reviews.freebsd.org/D47303