Log BasicThread timing information

- Log information about the actual and requested rate of a thread, plus
  the average time for doUpdate, and the percent of time spent sleeping.
  This information is logged as INFO.
- Also, move the logger from the component manager up to the basic
  thread.
- Switch all thread logging from the default logger to the thread's
  logger.
Turn on cpplint runtime/references

Turn back on cpplint's references checks, and fix the associated
warnings about passing non-const references where possible. Added
//NOLINT for situations where we interact with external libraries and
can't fix (YAML, OSG).
Fix non-const reference in DataGroupCopier

The DataGroupCopier was taking a non-const reference in its constructor.
And then holding on to the refernce as a member variable. Probably not a
great idea. This changes the non-const reference to a pointer, but
doesn't hold on to it. You need to re-pass the source and target to the
copy, which is a bit safer. However, it does mean that you need to be
sure the IndexDirectories of the source/target passed to the constructor
is the same as the ones passed to the copy. This is a bit better then
before, where the copy needed the inputData reference it was passed
during construction to be the same object as the one passed during
handleInput. Which it is in practice, but the interface suggests it
could be different (it passes inputData to handleInput).
Merge branch 'feature/thread-timing-info' into 'master'

Log BasicThread timing information to INFO

+1: Ryan Beasley, Gughan Sathyaseelan, Wesley Turner

Merged-on: https://www.assembla.com/code/OpenSurgSim/git/merge_requests/1354093
Merge branch 'fix/parameter-references' into 'master'

Enable cpplint parameter reference checks

+1: Harald Scheirich, Ryan Beasley, Julien Lenoir

Merged-on: https://www.assembla.com/code/OpenSurgSim/git/merge_requests/1363793
update yaml-cpp in External_yamlcpp.cmake
Merge branch 'fix/update-yaml-cpp-md5' into 'master'

update yaml-cpp md5 in External_yamlcpp.cmake

Merged-on: https://www.assembla.com/code/OpenSurgSim/git/merge_requests/1370503