Also remove 3rdparty_upstream from from submodules, accidentally
added in https://codereview.qt-project.org/#change,67241


This fixes init-repository.py.

Change-Id: I08c095e4830581156efc3f069e00e733dda1ffd8
Reviewed-by: Adam Kallai <kadam@inf.u-szeged.hu>
Reviewed-by: Andras Becsi <andras.becsi@digia.com>