Mainly a big merge into dev. This patch also contains:
- Fixes so bullet compiles.
- Fix a start up deadlock race condition in ConnectionManager.
- Fix some places where switching to Scoped joint names not complete.
- Major refactor of JointController::SetJointPosition. It's now much cleaner.
- Added set_joint.cc and set_pose_loop.cc for testing purposes.
Hard to break up the merge into smaller patches because most of the changes came from different merges upstream.