added files used to create reference and threat model diagrams

Removed Redundant Files

Added a example protocols folder for example/learning protocols not featured in the final implementation

 + Fixed Permissions bug
 + Attached example protocols
 - removed redundant files

Merge branch 'master' of https://git.soton.ac.uk/mwh1g17/Recommending-and-modelling-optimal-security-practices-for-smart-grid-connected-IoT-devices

Designed the NIST section to better describe how the project follows each of the five steps

Updated the research and design section to include the creteria for the scyther development enviroment and a comparison of Vagrant and OVF against this criteria

Added headings for Vagrant sections and expanded upon vunerablities

First complete iteration of the scytherbox, files contain all the information required to install the scytherbox virtual machine using vagrant

- Added before and after to message encryption protocol
- Added design for password policy protocol