C++11 roll-out and code clean-up.

[rrumpf]

This is a catch-all feature for code scrubbing as a go through, which includes the following:

• C++11 method usage on STL containers (e.g. emplace).
• Adding in this prefix to class variables.
• Addressing sundry TODOs as seen in the code.
• Attempting to move to a more algorithm-related model instead of for loops.