Fix some warnings.
Remove deprecated constructors for EmbeddedGraphDatabase.

o Use GraphDatabaseFactory instead.
Fixes problem with collection index types
Merge pull request #1403 from benbc/2.0-kill-off-more-deprecated-stuff

2.0 kill off more deprecated stuff
Merge pull request #1409 from systay/collection-index-type

Fixes problem with collection index types
Ensure ClusterRule creates a fresh directory per test method

o Removes unused protocol.cluster.ClusterRule
Fixes failing HA Index Schema IT in windows.
Fix the PMD warnings that failed Outreach.
Merge pull request #1411 from chrisvest/fix-pmd-warnings

Fix the PMD warnings that failed Outreach.
Creates an Advanced Usage part.
Merge pull request #1414 from jakewins/fix-schemaindexhait-win

Fixes failing HA Index Schema IT in windows.