Something like that. You could either have a little daemon that watches a file and flies it when it changes, or you could do it straight from the configuration management tool. For example, in Ansible you'd write a handler which is triggered after updating a copy of the pipeline file somewhere:

http://docs.ansible.com/ansible/playbooks_intro.html#handler...

The handler could use the command module to run fly:

http://docs.ansible.com/ansible/command_module.html