Updates and cleanup

Updates and cleanup

- Routing:
  - Use TreeRouteStack instead of SimpleRouteStack
  - Do not pull router from locator; simply instantiate
  - Config object can now be passed directly to addRoutes
- Bootstrap:
  - Accept ModuleManager as sole constructor argument, and pull merged
    configuration from it
- index.php:
  - Do not use object notation for accessing config values; use array
    notation. Allows flexibility in how application configuration is
    returned