Bump sbt from 0.13.2 to 0.13.6

I bumped sbt version to 0.13.6 (latest stable version) and remove all the deprecation warnings. 

- Since I've not figured out how to use `project/Unidoc.scala`, I haven't checked it works as expected although I just fixed warnings
- I guess ls-sbt is unused now (just add TODO comments)