Unify code from tuf/client and notary/client

[cyli]

As per discussions with @endophage, the client has a lot of code to read a repo from remote and local, and notary client has the code to write to remote and local (although there are redundant sections where both read from local cache).

It'd be good to just unify the common functionality in both.

[riyazdf]

Just noticed we have a duplicate issue #562. Will close this issue since that issue has more up-to-date dependencies