API: Improve error handling & introduce messages node in json responses

• Return all errors as json under an "error" root node.
• Introduce error handling in some places
• Introduce a default response structure

{ 
  root: {
    data: {
    },
    messages: {
    }, 
  },
}

• Remove set_x_messages and move messages into the newly added messages object of the response
• Extend specs

closes #383 (closed)