[Pipeline] Change `ci/checkforupdates.sh` due to local runners

We are deploying local runners for the pipelines. We found out that by default Gitlab mounts a volume with local repositories that may be already initialized; and it's possible that "upstream_repo" is already configured. This commit changes the script so that upstream_repo is re-used if it already exists.

An alternative is to always clean the docker cache after each set-up (https://docs.gitlab.com/runner/executors/docker.html#clearing-docker-cache) but this is inefficient as it will lengthen execution times.