Make CodeIgniter and expression engine works.

As described here https://github.com/aws/opsworks-cookbooks/issues/153 it make no sense that opswork create those symlinks for a php project because it's a Ruby on Rails standard. At least, 'log' and 'config' can make sense, but 'system' create problems with the well-known php framework Codeigniter and it's CMS, ExpressionEngine.