In an effort to have less to remember, the commands have been shortened
were possible. In some cases they have been moved around to organize
them so they are easier to remember.
This commit modifies the instruactions so that
they use the vagrant user instead of root. Also sudo is now
requierd for a significant amount of the commands.
The main purpose of this update is to make sure the guide still works with the newest version of all software. In running through the guide I found places to make bug fixes and minor improvements.