Update the code comments according to the new API in Server.scala

[Ayybeeshafi]

Code comments are not up to date to current implementation of the API.
For example:

**
    * Called to stop the instance with the specified id. The associated docker container is stopped. The Id is passed
    * as a query argument named 'Id' (so the resulting call is /stop?Id=42).
    *
    * @return Server route that either maps to 202 ACCEPTED or the expected error codes.
    */
  def stop(id: Long): server.Route = {
    authenticateOAuth2[AccessToken]
("Secure Site", handler.authProvider.authenticateOAuthRequire(_, userType = UserType.Admin)) { token =>
      post {
        log.debug(s"POST /instances/$id/stop has been called")

The log is up to date /instances/$id/stop whereas comments are outdated /stop?Id=42.

[johannesduesing]

Closed with #107