Add initial composer.json

- Include basic requirements for Kohana and Jam.
- Suggest other jam packages.
- Clear cache after install.
- Create:
   * application/classes/Controller/
   * application/classes/Model/
   * application/views/
Add application/logs and application/cache with 755
Add .gitignore

Ignore /vendor/ and modules installed via Composer.
Add bootstrap for different environments and routes.php
Add public folder with index.php and .htaccess