Migrate dependencies, depmap, detect_duplicates and check_published_deps to new options

Testing Done:
https://travis-ci.org/pantsbuild/pants/builds/39655628

Reviewed at https://rbcommons.com/s/twitter/r/1269/
Sync of https://github.com/pantsbuild/pants/commit/2cee9ffb825757cbe8cacfa23f305b3ad8d527ed