gitlab-shell: Access denied for git command <git-upload-pack...

Today, I found an issue that some user cannot clone(e.g. Using deploy key to clone):

Cloning into 'xxxxxx'...
GitLab: The project you were looking for could not be found.
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

Looking into /var/log/gitlab/gitlab-shell/gitlab-shell.log I can see this WARN everytime I trying to clone
W, [2018-03-27T18:41:53.387613 #6202] WARN -- : gitlab-shell: Access denied for git command <git-upload-pack 'xxxxxxxxxx.git'> by user with key key-11.

I found someone has the solution for this:
https://github.com/gitlabhq/gitlabhq/issues/5812

It looks like we not override gitlab_url correctly setting here
https://github.com/sameersbn/docker-gitlab/blob/master/assets/runtime/config/gitlab-shell/config.yml#L16

Could this be the issue? I change the setting in the config.yml, and now confirm this is the root cause

Start with assets/runtime/config/gitlab-shell/config.yml, especially the gitlab_url setting, and review the linked GitLab Shell configuration issue for context. Reproduce the deploy-key clone and inspect gitlab-shell.log; done means the clone succeeds without the access-denied warning.