Extend Configuration class to be able to load configs from files in repository
Move project configuration pieces into ProjectConfiguration

I originally was opposed to this because it exposes
some of the private workings of the base class to the inheritance chain,
but I decided it was worth the trade off for a cleaner interface in the base.
There is also the possibility that some other use will arise for being able
to define ones own implementation. Possibly a json to INI extension?
Migrated hooks to use Configuration and Git\Commit

This gets rid of dependence on the legacy $hooksConf free form INI

Moved a few to Deprecated since we longer use them,
but they may be useful for reference for anyone else who wants to convert them
Use a temlate for JIRA comment hook action
Finish migration of GitHookController to better configurations and object model
Fix name so that it parses properly
Getting started on unit tests for GitHook package
Allow a backdoor in case of emergency or broken hook configuration
Finish fixing remaining tests in GitHook package
Refactored Configurations package to support testing ProjectConfiguration