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.
Removed ZK.
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.
Catch up CHANGES.txt for recent deprecation removals.
Fix for leaking file handles for rrd db on server startup timeout.
Switched StoreID to not use current time as random seed.
Merge pull request #1444 from jakewins/die-zk-die

Removed ZK.
Fixes ha-robustness issue with dangling dynamic records.
Improvements focused around Cypher 2.0.
Move the Java REST tutorial inside the Languages chapter.
Merge pull request #1447 from jakewins/rrdb-leak

Fix for leaking file handles for rrd db on server startup timeout.
Remove the legacy setting for cypher parser.
Do not read from non-recovered store files.

During recovery, reading from the store files is not safe, since they
might be in an inconsistent state until the store has completed the
recovery phase. The transaction log does not contain information about
data that did not change though, so rebuilding indexes requires reading
from the store files.

These changes defer the reading of the store files for the purpose of
rebuilding the indexes. We keep a running set of which nodes have been
updated by the commands in the recovery processes, and at the end of
recovery we drop any information about those nodes from the indexes, and
rebuild them by reading the current (final, consistent, and stable)
state of each changed node from the store files.
Merge pull request #1448 from thobe/2.0-do-not-read-unrecovered-store

Do not read from non-recovered store files.
Clean up some warnings.
Remove deprecated WebServer#addExecutionLimitFilter(int, Guard).
Consistency checker: verify that nodes in the node store are in the label scan store.