Tracking down a strange bug report. Fixing some output. Fixing some samples.
Cleaning up RNEMD log, adding XY area to Snapshot
Adding new RNEMD options and output file format
Code readability updates.
Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
Reorganized source directories, added RNEMD and flucQ blocks for options parsing.