Create Server subpackage

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 (closed)