Makes CommonDevice's DataGroups private.

Now the accessors must be used for a subclass device or its scaffold to
access the device's m_inputData, m_outputData, or m_initialInputData.
Removes unused constructor for NamedData.
Adds UnitTest for contstructing NamedData from IndexDirectory.
Removes unnecessary local variables in PoseIntegrator::initializeInput.
Moves definitions of CommonDevice member functions to cpp file.