Puppet db setup

This branch requires [#738] as a prerequisite.

Fixes to the Vagrant setup as follows:
- Fixed paths puppet because api is now a sub-module.
- Turned off tests to improve loading time for vagrant users.
- Fixed database syntax error for patching the database.
- Updated documentation to reflect test suite now disabled.
- Updated documentation to include required instructions that were in the "notes".
- Improved formatting of README file.