Changed Manifests to ClassTags as much as is possible in commands. There...

@casualjim This is the change to manifests I talked about before. The code doesn't compile yet, because of the issue with Swagger still using manifests (and some massive Manifest Factory that was made due to issues with reflection in Scala 2.10.x, which this version of Scalatra won't support)

Once Swagger gets changed to use TypeTag/ClassTag, or macros through something like https://github.com/crypticmind/scala-swagger-modelgen we can integrate the code together.

The change to ClassTags will also fix issues such as using top level classes, as well as future proofing the code more (Manifests are deprecated)