the looping structure for RUN_NUM now occurs in AbstractAnalysis, so
that the sequencing is correct - a few related variables were not reset
- so those are fixed now too.
* removed unused and unneeded classes and added the ones that were
missing
* put the most recent graphics code into David's great structural org!
current issues:
* the config file is still not loading at the start of the code (only
in RefractiveIndex.cpp does it work - not in main.cpp - where the 'full
screen', etc. are set
* the analyses being called in RefractiveIndex.cpp always run the first
listed one twice - weird!
* the saving (NUM_SAVE_PER_RUN) and frame (_frame_cnt_max) conditions
are competing - can we relate them?
