Remove some deprecated methods in GraphDatabaseAPI.
Removed deprecated consistency check main class.
Remove deprecated things in the server component.

o Changes Database to be an interface, things piggy-backing on the Database class
  for shipping dependencies around now are assigned those dependencies directly.
o Removes a few small deprecated things in for instance NeoServer.
Merge pull request #1418 from jakewins/deprecated

Remove some deprecated methods in GraphDatabaseAPI.
Merge pull request #1441 from jakewins/more-deprecated

Remove deprecated things in the server component.