Prior to this change, all proto definitions were in the root of this
project. Creating one big package, and confusion. For example, myself
and others expected each service to be a namespace, so the
RepositoyService::Exists message was a different one from
NamespaceService::Exists for example.

This change *copies* the server proto to a package directory. Having a
separte directory for each package or module/class is not a neccesity,
but it given this is the usual way of doing it in multiple languages it
seemed the cleanest way to signal a serperation of concerns.

Given the structure of the repository changed, the ruby script
generating the proto defintions has been changed too.

Changes are needed for: gitaly#655