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).
Oh, I see what you're saying :)

I don't think a name change buys us that much unless we also write something to convert old to new.