I've just updated from 9.0RC3 to 9.0-stable r229626 after a clean
install. However when trying to add the first packages I noticed that
pkg_add is installing packages from
ftp://ftp.freebsd.org/pub/FreeBSD/ports/amd64/packages-9-current/ and
not from package-9-stable which I would expect. In particular because
the package-9-stable directory does now exist on the server.

Using Google this appears to have to do with
/usr/src/usr.sbin/pkg_install/add/main.c in which the following
revision appears to include the link:
http://svnweb.freebsd.org/base/head/usr.sbin/pkg_install/add/main.c?r1=225757&r2=225756&pathrev=225757
However if I look at this specific source file on my system line 98
that brings in the link to packages-9-stable is missing (The file has
packages-9.0-release, but not packages-9-stable)

Any suggestion on what I am doing wrong would be highly appreciated as
I don't understand this.

*) uname -a shows 9.0-stable r229626; the update to latest stable has
been done according to handbook. No variables that could affect this
have been changed as it was a clean install using the 9.0RC3 bootdisk
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