Allow the use of events at the beginning and end of the run; this should have almost no effect on LB data (since we're using solicited triggers already), and gains valuable statistics in noise runs.
Extend the run ranges used for noise generation to include Run2c, and add a special noise window for the 9-28-2011 APD biases.
Make SafeStopwatch a header-only class.  Also, make it thread-safe even if USE_THREADS is undefined; this simplifies code and shouldn't hurt in any case.
Place denoising results into a vector within EventHandler rather than a local vector.  Step 1 of letting us maintain entry ordering.
Create a new EventWriter class which handles ordering of events by entry number, grabbing from the processed file, and writing into the output file.  Better modularization of code, and also implementing the ordering as a new feature.
Correct a mistake in the APD gain.  I had used the u-wire shaper gain accidentally.

This provides a roughly 75% correction factor on the gain, which influences the Poisson-to-Electronic noise ratio.  In testing, this seems to particularly improve the MS resolution, and has been demonstrated to improve SS resolution slightly as well.
Bug fix -- channel 163 was only disconnected in February 2012, but I was forcing its gain to be identically zero.  That would cause it to be weighted too heavily in signals, with its Poisson noise underestimated.
There is not readily-available laser data for gang 163 because it was disconnected before the first new-style laser run, so I've just used a dummy value of 200 to make sure it's on the right rough scale.
Permit (force at the moment, unfortunately) a non-default gain correction factor from the input file; used to see if resolution is significantly non-optimal where I am.
Changes to noise correlation code to make it:
Compatible with changes to EXOCoincidences.
Use all LB events available.
Print output which is more useful to judging progress.
Changes and updates to the MakeInFiles sample script.
Realized that we needed a new noise window, since the noise characteristics changed after the cleanroom temperature excursion in early September 2013.