Use Click instead of Flask-Script for CLI commands

- Update Flask to 0.11 (with built-in Click integration)
- Remove manage.py
- Add autoapp.py per Flask doc's new recommendations
  for using Click with an app factory
- Define cookiecutter-flask's commands in cli.py
- Register shell context and shell commands as part
  of factory-based app creation
- Update README instructions with examples for running
  commands in new Click style