Re-expose mysql port and pass along the username and password.

Passing in the username and password could be useful for setting
the username and password in a wrapper script for starting mysqld
later. For now it provides the environment variables for the php
container to grab from getenv();
Adjust note about how to connect with application.
Add looping logic for arbitrary containers in provisioner.

Allows user to define their own containers with dockerfiles. Also
implements a check for remote copy, and pulls it down.
Add checks for already-running containers.
Add a restart if a container is already running.