Update gitaly default config to be useful as a GitLab CI service

Updated the gitaly config with some of the fixes we have used in the charts to the path.

Also updated the copy command for shell to chown the files as the git user. (The directory is already owned by git in the upstream shell image) We do this so files in that directory can be modified by the running user. (For example, remove all the shell hooks during testing)

See https://gitlab.com/charts/gitlab/issues/826 for more details on why we need these changes.

cc\ @nick.thomas