Update github url

https://developer.github.com/changes/2014-04-25-user-content-security/
Add note on broken net-ssh version
Add HOST to deploy_to

alaveteli is only used when the install script is run with the --default flag. Otherwise, it uses the HOST param or the EC2 hostname.
Add instructions for setting up authentication of deployment user
Add leading slash
Add link to SO for net-ssh bug
Remove un-needed backticks.
Make it clear that the last few commands are run on the server

Also tell people to restart MTA
Add instructions for updating Alaveteli path in init scripts.
Add some details about config for thin.
Merge branch 'portugal-workshop-fixes' into gh-pages