Update setup.asciidoc

Add a note about using the same JVM version on all nodes and clients
Fix TransportNodesListShardStoreMetaData for custom data paths

Cleans up the testReusePeerRecovery test as well

The actual fix is in TransportNodesListShardStoreMetaData.java, which
needs to use `nodeEnv.shardDataPaths` instead of `nodeEnv.shardPaths`.

Due to the difficulty in tracking this down, I've added a lot of
additional logging. This also fixes a logging issue in GatewayAllocator
[GEO] Throw helpful exception for Polygons with holes outside the shell

A recent situation occured where a MultiPolygon coordinate array was accidentally defined as a single polygon with multiple holes. Since the intent was a MultiPolygon, the holes of the unintended Polygon fell outside the outer shell.  This exposed a bug in the contains logic inside BasePolygonBuilder. An ArrayIndexOutOfBoundsException was being thrown instead of a more useful ElasticsearchParseException( "hole is not within polygon" ).  This pull request fixes the bug and adds additional unit tests for verifying proper MultiPolygon type parsing.

closes #9071