Implement more robust handling of config stages in Application

[Brian Granger]

Currently, we have various stages of config in our Application class. We need to refactor this to simplify the logic:

* Create a bootstrap config object that contains things like ipython_dir
* Have a single self.config object that hold the current state of the config. All code in Application should use this
as the single source of config data while Application is being initialized.
* As each config stage is completed, the config will always be merged into self.config.
* We need to implement configuration key freezing to allow an Application to disallow particular config keys from
changing.