Added the ROOTLIB flags to the library compile statments in the
common.mk file.  This is necessary for the interpreter to be happy
with the LendaFilter object which contains TMatrixT objects.  The
executables appear to complie without the flags but the library
cannot be loaded into a ROOT session without them.
Commented out the Evt2CalStatic building rules and target statment
Changed the TMatrixD statments in the filter class to TMatrixT<Double_t>
Statments.  Made the filter a ROOT class.  Inherites from TObject now,
has a LinkDef file, has ClassDef statement in the header file.  Make
file has been modified so it builds the Dictionary
Fixed the makefiles for the LendaPacker.  Now it includes all the
other libraries and has -Wl,rpath statment to link the libraries.
Root was insiting on this in order for LendaPacker to loaded into
the interpreter
Removed reference to the un_ordered map library
Added the new libraries (Filter and packer) to the root start up
script in the skelton user.  Fixed small bug in Logon script
Added the Packer Linkdef to Repo.  Added UpdatedUserSctipt
sctip to the repo.  Will loop through the users and remove
the logon file and re-logon to that user.  This will put
the latest version of the logon and logoff scripts into
each users account
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