OGM-424 Adding test for auto and manual flushing for JP-QL queries
OGM-424 Auto-flushing for native queries executed via classic API

* Also adding test for executing native query via JPA
OGM-424 Adding note on flush modes to MongoDB chapter in reference guide
OGM-369 Re-enabling test
OGM-574 Extracting dependency management information into separate BOM POM
OGM-574 Updating "Getting started" guide
OGM-574 Removing some unnecessary dependencies
OGM-574 Consistently using JTA 1.2
OGM-574 Updating some dependencies
OGM-574 Moving JTA dependency to BOM as it's referenced in the "Getting started" example