fixed indentation in aps_extractor.h
start commenting aps_extractor.h
removed unused argument from plot_thinned_data
removed unused arguments from write_good_points and draw_bayesian_bounds
explained the purpose of all of the public methods in aps_extractor.h
removed unused variables from make_boxes
documented make_boxes
finished documenting aps_extractor.h and aps_extractor.cpp