Update run script

 - The repository is now in the form of http://flapjack.io/docs/1.0/development/Packaging/
   - Due to the way aptly works, all components must be published at the
     same time, even if there are no packages in them.
 - Work out the major version of Flapjack from the version string, and use that for the
   repository prefix.
 - Create directory listings from the public directory, so the paths are
   correct.
Merge branch 'omnibus3-aptly' of github.com:flapjack/omnibus-flapjack into omnibus3-aptly