Fetch repositories with --prune option by default.

This will allow us to not recreate branches that has been deleted on the upstream and the mirror.

Related issue: https://gitlab.com/gitlab-org/gitlab-ee/issues/1277

I've reviewed the code for updating local and remote mirrors also I've manually tested these features and all looks good.

Here is the description of the --prune option:

--prune

Before fetching, remove any remote-tracking references that no longer exist on the remote. Tags are not subject to pruning if they are fetched only because of the default tag auto-following or due to a --tags option. However, if tags are fetched due to an explicit refspec (either on the command line or in the remote configuration, for example if the remote was cloned with the --mirror option), then they are also subject to

@brodock do you see any issues when fetching repos for GitLab Geo?