Fix VM provisioning of application.

Added missing dependencies (php and php Apache module), got rid of the
multiple stages of Puppet since they were causing some nasty and
unexpected (and undebuggable) behavior.

Also, for all package installation, made sure an `apt-get update` is
executed, preventing Not Found package hits.

The README was updated to reflect the changes, removing the requirement
of composer (and its dependencies) instalation.
Less uglier overlay for "gravata".

It doens't mean it is pretty now, but it has no white borders and it is
less pixelated.

It still sucks, but I tried.