Various Windows compilation fixes
Fixed a bug in ForceManager and a compilation issue for cygwin
MERGE OpenMD development branch 1465:1781 into trunk
Code readability updates.
Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
Fixing some bugs in optimization, fixing status functions so that they dump correctly (although some things are deferred until the Stats is accumulator-based).
fixed an uninitialized option bug, fixed gcc 4.6 compilation problems
fixing some bugs, adding Shake
fixes to minimizer parameters, start of intermediate status output for minimizer.
added a minimizer parsing block
Adding initial import of optimization library