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).
If you want to more tightly scope the variables you can use an if/else:

if version, ok := typeNamePathToVersion[key]; !ok {
  // error
} else {
  return version, t.Name(), nil
}