Deprecation notice about gitaly['storage'] shown even if user hasn't explicitly set it

Because our library sets gitaly['storage'] from git_data_dirs in https://gitlab.com/gitlab-org/omnibus-gitlab/blob/d5c45bd922191c5057cc23f1899c92c8365b6d70/files/gitlab-cookbooks/gitaly/libraries/gitaly.rb#L96, and because that setting has been deprecated in !6621 (merged), users will see a deprecation notice about it.

We should use the new format to set the configuration.