New Correlator; **GeProcessor still has an issue; Other bugs fixed. Issue with Globals class.
The ScintProcessor has been split into the three components, the detector
types/subtypes will stay the same (scint beta, etc.)

Globals.xml:
The new xml file that holds all the information about the Global constants.

Makefile:
Updated to scanof.f, removes the need to link against the acq2 libs.
Also, arranged and organized the object files for easier addition. Added
the tidy recipe to clean things except the executable.

BetaProcessor:
Handles things related to beta scintillators.

DammPlotIds:
Rearranged and moved some of the namespaces.

DetectorDriver:
Implementation of the new Correlator. Old one is broken.

EventProcessor:
Changes related to the new Correlator.

FittingAnalyzer:
New fitting routine, produces more accurate results, better resolution.

GeProcessor:
Overhauled to fix the numbers of the histograms, as well as some bug
fixes. ******NOTE****** There is still a problem here with some spikey
spikes in the gamma region of 2400-2800 keV in the calibrated gammas.

Globals-bkp.hpp:
This is a backup of the original Globals file. It will be removed after
the transition to the new globals scheme.

Globals.hpp:
Class header for the new Globals class.

IonChamberProcessor:
Moved the declaration of the spectra.

LiquidProcessor:
Handles liquid scintillator detectors.

LogicProcessor:
Combined the TriggerLogic and Logic Processors. TriggerLogic called
everything in the logic processor, including both made no sense.

MapFile:
Things were changed in order to make way for the new correlation scheme.

MtcProcessor:
Added the PreProcess for the new correlations.

Neutron Processor:
Handles a generic neutron scintillator.

Places:
Handles part of the new correlation scheme.

Plots:
Fixed problems with the PlotsRegister singleton, and updated the handling
of the duplicated damm ids.

PlotsRegister:
Fixed problems with the singleton definition. Memory leaks seem fixed.

RawEvent:
Added information for the usage of the new correlation. Moved energy
contraction parameter

ScintProcessor:
Still hanging around for legacy reasons, will be removed once the Beta,
Liquid,Neutron processors are a go.

TimingInformation:
Added some new parameters for the timing analysis. *****NOTE***** This
class needs rewritten terribly.

Trace:
Added in new stuff related to timing analysis. Fixed some issues with
return variables.

TraceFilterer/Plotter:
Added in some stuff for the PlotsRegister.

TreeCorrelator:
Handles the new correlation scheme.

VandleProcessor:
Added in some information to calculate the walk in the betas, also some
general cleanup/fixes.

pugi*:
The files used to do the xml parsing for the new Globals class. These are
included under the MIT license.

map.txt:
Removed due to incompatibilities with the new correlator.


Signed-off-by: S.V. Paulauskas <stanpaulauskas@gmail.com>
Cleaned up base dir, fixed errors in Ge, Numerous other changes.

Many of the changes related to removing externs, splitting the RawEvent,
making the singleton classes, and cleaning up the base directory were
done by Krzys Miernik. The TreeCorrelator and associated files are
completely his as well. I have done my best to make sure that those
changes and improvements were merged properly. -SVP

The base directory was cleaned up and the configuration files were moved
to the config/ directory. There are two configurations that are
included here(73cu, leribss2011). By default the configuration is
73cu, as this is my testing setup. The documentation was moved to the doc/
directory. The problems with the GeProcessor have been sorted out, they
were due to a missing check for the saturation bit. Globals class has been
removed and will be implemented in a different way. Detailed summary of
changes follows.

.config:
This points the PathHolder to the right place.

Makefile:
Added flags for debugging, reorganized the object files, etc.

confg/*:
Nothing to report, these are just the moved files.

doc/Doxyfile:
Fixed the paths, added in some new things to be ignored. This should
probably be updated futher at some point.

BetaProcessor:
Removed the TreeCorrelator stuff

DetectorDriver:
The DetectorDriver is now a singleton class. This makes sense as we are
calling this thing a lot. The TreeCorrelator stuff has all been moved to
its own files. The calibrations now use the new path builder.

DetectorLibrary:
Updated to use the new singleton class. Also uses the new ChanIdentifier
class. Extern removal.

DetectorSummary:
This has been split away from the RawEvent stuff.

DoubleTraceAnalyzer:
Removing the extern

EventProcessor:
Changes to use the new scheme. Removing externs.

Exceptions:
Handles some error messages, this will be expaneded later to include
error messages from processors, analyzers, etc. This should help make
debugging things easier.

FittingAnalyzer:
Added in a catch so that traces without any found waveforms do not get
analyzed. Fixes a problem that caused a segfault.

GeProcessor:
This puppy has been completely overhauled again by Krzys M.. I have added
back in functionality regarding the saturation bits to keep the spikey
spikes from showing up in the gamma spectra.

Globals.hpp:
This currently holds a lot of the variables that are needed gloabally
within the program. It will be removed once the ParseXml class is
fully implemented.

Initialize.cpp:
This replaces the old DeclareHistograms file. It handles the
initialization of things in the program, and gets things kicked off.
*EVERYTHING* starts here.

LitePositionProcessor:
Updated to handle the new stuff.

LogicProcessor:
This has been combined with the TriggerLogicProcessor, as the
TriggerLogicProcessor simply called *everything* in the LogicProcessor.

MapFile:
Changes relateing to the new config stuff.

MtcProcessor:
Updated for the new TreeCorrelator

NeutronProcessor:
Changes for the TreeCorrelator.

ParseXml:
A class that parses simple XML files that are simply designed to hold
constants based on paths. Useful for the new constants handling. Also,
can be used for future upgrades to the cal.txt and map2.txt.

PathHolder:
Handles pointing things to the proper config files.

PixieStd:
Removed all the externs. Updated to use the new singleton classes.

PlacesBuilder:
Part of the new TreeCorrelator setup. Handles the creation of the "Places"
See description in header for more info.

Places:
Handles the processing related to the places built in the PlacesBuilder

Plots:
Removed the non-empty histograms list (not sure why, it was done by KM).

PlotsRegister:
Still a singleton, changed the method used to get the instance.

PositionProcessor:
Updated to handle the new scheme of things.

PulserProcessor:
Removed some of the unnecessary headers.

RandomPool:
This is now a singleton too.

RawEvent:
Broke Identifier, ChanEvent, DetectorSummary, StatsData into their own
files.

ReadBuffData.RevD:
Changed what the saturation sets things to, and added some new headers.

RootProcessor:
Updated to handle the new system.

StatsAccumulator:
Removed, only a single method used it, and that method was rewritten.

StatsData:
This came out of the RawEvent.

TimingInformation:
Some enhances for the new system. It works but is ugly, and I hate the
bastard.

Trace:
Some changes so that the StatsAccumulator could be safely removed.

TraceAnalyzer:
Changes for the new system.

TraceFilterer:
Changes to use the new config folder.

TreeCorrelator:
Updates to handle changes to Places, and PlaceBuilder

VandleProcessor:
Updated for the new system.

scanor.f:
The old version of the scanor program has been obselete for some time.
Robert Varner suggested using the new one. There seem to be no problems
at this time.


Signed-off-by: S.V. Paulauskas <stanpaulauskas@gmail.com>