[WIP] Pre-beta refactoring

## Goal

This refactoring has several goals:

# Change the structure file to a serialize object graph to enable:
  
  # A better integration with twig
  # Faster inheritance
  # More flexible back-end

# Improve DIC Wiring in Application class to be able to improve DI handling
# Rewrite the default template in Twig and thus fix bugs related to the template
# Integrate Twig into Core
# Deprecate all XML related behaviour

## Tasks

This is not an exhaustive list as a lot of the refactoring has already been done before I discovered this feature in Github.

[ ] Write XML output Writer
[ ] Create compatibility layer
[ ] Think about versioning in cache / object graph
[ ] Allow smart selection of serialization type
[ ] Clean up code
[ ] Write documentation
[ ] Elements should be related to files
[ ] Deleted files are not yet removed from cache
[ ] Refactor XSL writer to have a dependency on the XML writer