Remove some dead code.
[TEST] Wait for threads to finish / start before asserting
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