System.out.println -> Logging

Closes #715: Replaced all System.out.println() with proper logging
more refactoring in reef-io (logging, code style, minor fixes) - not finished yet
more refactoring in reef-io (still not finished)
Merge branch 'master' of github.com:Microsoft-CISL/REEF into weimer_715
Made all methods in ClientJobStatusHandler synchronized.

Reasoning: This is a defensive move. This class is not in the critical path performance wise, and synchronizing it makes reasoning easier.
Merge branch 'master' of github.com:Microsoft-CISL/REEF into weimer_715
Merge pull request #721 from Microsoft-CISL/weimer_synchronized_client

Made all methods in ClientJobStatusHandler synchronized.
Reduced the usage of ConfigurationFile
 * Removed all instances where it was only used to log. Those are replaced with the AvroSerialization's JSON output.
 * Removed a roundtrip test that is now better covered in Tang itself.
Merge branch 'master' of github.com:Microsoft-CISL/REEF into weimer_715
remove last references to the distributed shell from the retained evaluators unit tests; minor refactoring (use chained configuration builder calls) etc
Merge branch 'master' into weimer_reduce_ConfigurationFile_usage
Merge branch 'master' into weimer_715
minor fixes in AllReduceManager
more refactoring and cleanup in ReduceHandler. no functionality changes
remove unused nsPort variable in NetworkService constructor
Merge pull request #716 from Microsoft-CISL/weimer_715

The reported test failure is immaterial for these changes. Merging.
Removed all usage of ConfigurationFile and replaced it with ConfigurationSerializer
Updates according to code review
Update HelloCLR for using assemblyQualifiedName

Update HelloCLR for using assemblyQualifiedName
 * Updated YarnContainerManager to use ConfigurationSerializer.
 * Deleted FileUtils, as YarnContainerManager was the only user left