[Java] [Cosmetic]: 1. regenerated the SBE-IR classes after #166 and ...

1. regenerated the SBE-IR classes after #166 and suppress an extra new line from JavaGenerator.
2. added .apt_generated and .factorypath to .gitignore (these resources are used by the annotation processor configured in eclipse - jmh in this case)
3. cleaned up some warnings (added generics, added try-with-resource, fixed unused variables)