Fix deprecation warning about git_data_dirs

What does this MR do?

Deprecation logic works on node object, but we did not populate git_data_dirs on node object because at that time there was no need for it. But, we now have a need for it, and has to populate it there for deprecation warnings to work properly.

Testing

1. On a default instance, confirm no warnings are shown at the end of gitlab-ctl reconfigure run.
2. Edit /etc/gitlab/gitlab.rb and add the following to it and run reconfigure.

   git_data_dirs(
     {
       "default" => { "path" => "/var/opt/gitlab/git-data" },
       "alternative" => { "path" => "/mnt/git-data" }
     }
   )

   1. Ensure warning is shown at the end of gitlab-ctl reconfigure run.
   2. Ensure /var/opt/gitlab/gitaly/config.toml has the alternative storage in it.
   3. Ensure /var/opt/gitlab/gitlab-rails/etc/gitlab.yml has alternative storage in repositories.storages key.

Related issues

Closes #8960 (closed)

Checklist

See Definition of done.

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