Decode/Encode everywhere

Necessary for Brendan's upcoming api versioning PR. This is a fixed version of #567.

All types stored in etcd are now API objects.
>This means I made an api.ContainerManifestList, and added a JSONBase to endpoints (and changed Name to JSONBase.ID).
Lol, actually not, this was intended to be documentation. Clearly not good documentation, so I removed. But #672 does add other documentation.