3.0 Shell cleanup pt.1

This is the first set of changes for #3325. I've removed a bunch of CLI flags that were used to support global CakePHP instalations. Since we are only going to be supporting local per application installs for 3.0, we no longer need a way to set the app/working/root. They are always defined by the application constants.

I've also removed the CLI stubs from this repo as they are non-operational.

I'll be opening a pull request for cakephp/app as well.