Feature release

Alpha pre-release supporting major feature update. This release is backwards
incompatible with previous releases, and requires a revised data directory
layout.

• Added sequence and variant annotations (which introduces a sqlite
  database component)
• Added repo manager, a command line tool to manage data files and
  import them into the server's data repository
• Supported searching over multiple ReadGroups, so long as they are
  all in the same ReadGroupSet and all of the ReadGroups in the
  ReadGroupSet are specified