Added CorrectedSoftTopTOF and CorrectedSoftBottomTOF to the LendaBar
Class.  Added a GetCorrectedAvgSoftTOF method to get the average of
the softwareTOFs
Added a corrected SoftwareTime to the lendaChannel class.
Added a Software Reference time to the LendaChannel Class
Added some comments to the LendaPacker Header.  Added another small
Container class to hold the 3 different types of reference times that
a channel can have.  RefTime RefSoftTime RefCubicTime

Added several new methods for restructuring.  DDASChannel2LendaChannel now
calls the filter methods and fills basic information.  Then it calls
PackCalculatedValues to pack the results of the Trace Analysis into
the lendaChannel.

Added FillReferenceTimesInEvent which Packs the event and sets the
reference times in the underlying channels
The implementation of the changes discussed in previous commit.
The packing is slightly more modular to allow the repacking methods to
call the same bits of code when repacking.  There is now ReMakeLendaEvent
which will take the LendaChannels in the Bars and TheObjecScintillators and
Call the RePackChannel Method on them.

At the Momement RePackChannel and will Get the map info for the channel,
recalculate the waveform analysis routines then call the same PackCalculatedValues
method that the intial packing calls.  It is doing this on the inEvent data.

ReMakeLendaEvent

Recalculates the values for the calculated values in the inEvent.  Copies
each bar over into a temporary map (Just as the initial packing does).  Loops
over the objectscintilators and copies them over to outEvent
and then Calls RePackChannel. Stores the ReCalculated Reference times in the
same type of structure as the initial packing.  Then calls FillReferenceTimesInEvent
where the bars are copied over from the temporary map to the outEvent structure.

NOTE: Currently ignores any channels in the UnMappedChannels vector.
NOTE: Calling the method will change values in inEvent
Added 2 new scrips to the general scrips directory.  FileCompare and
PlotEres.  FileCompare will loop over two files and compare the entires
right now it just looks at the lendaevent->N parameter.  Soon I will
implmented a ==operator for the lendaclasses.  Plot ERes expects that
you are in a file with output from the timing analyzer.  Will take a
2-D histogram and make a Resolution vs pulse amplitude plot.

The Timing Analyzer is under construction
Added comparison operators to the LendaEvent class structure.
At the moment the lendachannel class will check that everything
is the same except the trace/filter/cfd. The LendaBar class
will check all the channels and the quantities that it calculates
like Dt, AvgTOF...

LendaEvent will compare all the bars, all the object scintilators and
all the UnMappedChannels.  Will also check things like N, NumBars...
ect.
Changed FileCompare to use the == operator in the event.
TimingAnalyzer is a work in progress.
Comparison for file checking is a work in prgoress.  Added method to
Channel class to print the two channels values next to each other
when they are not equal
Save traces on
Added the better GetEnergy method that was on the OPT branch.
Instead of integrating the whole pulse, it takes only a window
around the maximum value.

Renamed all the get*** Methods in the Filter to Get***.  GetPulseHeight
methods now take a second argument to save the max height spot for
the new GetEnergy.

I think I have solved the problem with the short and long gate filters.
Thought there was a difference between the RePack branch and the Master
branch, but there was the same bug in both.  The Long/Short gates would
start a few clock tics away from the softwareCFD value.  When the Get
Zero crossing method would fail it would set softwareCFD to -10008
Then the Long/Short gates would start at -10000ish value and add
up gibberish.

Now the Long/Short Gates start at MaxSpot-4.  This way it won't
can't fail to find a start point and so it won't add up gibberish
GetStartForPulseShape checks to see if MaxSpot-4 >0.  If it isn't
returns 0.

Changed the CalcEnergy Filters method in the Packer to use the better
GetEnergy method and to use the better GetStartForPulseShape Method.
Removed Check on Long/Short Gate for == operator in LenaChannel
Changed the SyncDt in the bar class to use the Corrected Times
instead of just times.
Added the new Graph LE Script
Changed the comparison methods to make a sensical comparison of
this branch vs the master branch.
Merge branch 'RePack'

RePack has Re-Organzied version of the Packer Class which makes it easier
to run time analyzer.  Alows for ReMaking of lendaevents from other
lendaevents.  There have been other changes as well. See previous
commit messages
Turned off Save traces in packer.  Fixed thing in build data
Added the Calibrate program to the repo.  Seems to work pretty
well.  Needs some code clean up at one point
Renamed the Skelton directory to the proper spelling (i hope).
The Corrections files for the test run have been changed to
the most recent version of the calibrator output
GraphLE script now puts Trace,Filter,CFD in the graphs title
LendaBar now has a BarAngle parameter.

LendaPacker now has the infastructure for setting the bar angle in the
event building.  The MapInfo class has a bar angle parameter.  The Make
LendaEvent method sets the bar angle in a similiar way that the bar
name is set.  Don't think that it will set the bar angle in remake
lendaevent.  Need to Check that at one point.

Also The packer now has a method to get the map info object for a
given channel.

Changed the GetZeroCrossing calls to GetZeroCrossingImproved calls.
See next commit for the difference