Dockerfile works properly, documentation updated

- Dockerfile now builds properly
- Dockerfile now ADDs files from local directory. This allows
  you to either pull from github (for master) or to build
  locally (for development)
- Removes some dependencies from container (wget, git)
- Removes pulling apache virtual host file from github
- Upgrades MySQL start check to actually check instead of just
  sleeping
Merging in update patching branch

Conflicts:
	Dockerfile