Change Configs
Remove Apache Module
Add Apache Module as a Git Submodule
Remove Apt Module
Add Apt Module as a Git Submodule
Remove PHP Module
Add PHP Module as a Git Submodule
Remove PuPHPet Module
Add PuPHPet as a Git Submodule
Remove StdLib Module
Add StdLib as a Git Submodule
Change StdLib Module Version to 3.2.0
Revert MySQL Changes
Readme Updates

Change Some Test Config on Vagrant File