Major code update and restructure. Not compatible with older input files.

CCMD 2.0
* Convert use of pointers and loops to C++11
* Removed dependency on Boost for libraries now in C++11
* Restructured class and variable naming for consistency.
* Optional multithreading in Coulomb force.
* Removed unnecessary local copies of simulation parameters.
* Integration times now specified per cycle.
Merge branch 'master' of github.com:chrisrennick/ccmd

* 'master' of github.com:chrisrennick/ccmd: