Updated the input manager.  Now has some maps to specify what the valid options are

There are 3 different maps one for doubles bools and strings.  Looks for
inputs of form
flag:argument

added lean flag which uses the traces to calculate things but then does not save them in
filtered files
In Gamma builder added the %done and time remaining feature that I made in

Neutron Corrector.  Added the .hh files to the makefile so it will updat when I change headers
Added new flags to inputmanager.  Has lean and fast.  Lean doesn't save the traces/filters.  Fast
skips all trace based analysis.  Added flags for setting the correlation timewindow (timeWindow: )
and for the trace delay parameter.  Added a catch in the packEvent method for the presence of duplicates in
the event.  Ie more then one channel X.  Not seeing any of these events in the one bar data.  Will probably see
more with more bars.  Right now just says "crap" if it happens.