Improve Dependency Injection for NotaryRepository initialization

[endophage]

Currently it takes a basedir and a RoundTripper, this is fine for NewNotaryRepository which should be a simplified initializer with assumptions made. However, for unusual use cases and testing, it would be helpful to be able to inject a cache and RemoteStore directly.

We think this should probably be done by exporting repositoryFromKeystores (and maybe renaming it to something like NewRepositoryFromStores), and having it take an initialized cache and RemoteStore, rather than baseDir and rt.

[endophage]

Closed by #1094