Adds manual tutorial on how to use the new indexes via the core API
Added cross links in the manual around indexing
Updated CHANGES.txt\'s to prepare 2.0.M01
Updated shell/CHANGES.txt\'s to prepare 2.0.M01
Output passed as Writer to Cypher ExecutionResult now flushes on newlines via Output.println()
Merge pull request #633 from jexp/flush-shell-output

Output passed as Writer to Cypher ExecutionResult now flushes on newlines via Output.println()
Improved profiler output

o Removed ParameterPipe from every execution plan
o Start points have more information on index/label choice
Merge pull request #635 from boggle/entity-producer-profile

Improved profiler output
Make EphemeralFileSystem handle concurrent modification to its list of stored files.

- This was breaking SchemaIndexAcceptanceTest because of recursive deletion in a background job.
- Also removed awaitIndexState() helper method (replaced with awaitIndexOnline())