(PUP-1118) Simplify Puppet::Context

Puppet::Context can reduce the number of objects that it uses for
tracking contexts by keeping everything internal to it. This actually
results in much less code, but a few more instance variables to track.
Overall is seems like an easier to understand system.
(PUP-1118) Create a new context after app initialization

There end up being 3 steps of initialization in puppet:
  * bootstrap: after code starts loading, but before initialize_settings
    is called
  * initial: after initialize_settings is called, but before an
    application has been loaded and sets up the true run mode
  * application: after an application has started running, set the run
    mode, and reinitialized the app default settings.

This last one had been missed in previous changes to have puppet setup
the right contexts. This now setups another context override in the
Puppet::Application run method to control the application context.