Changed pulse arrays to vectors

Changed pulse waveform output from fixed size arrays to vectors of
integers. This allows the storage of multiple pulses per fill. All
pulses for a single event are stored in the same vector. The size of
the waveform vector divided by the multiplicity of the pulses will
give the size of a single pulse for later analysis.

Changed the name of BetaProcessor to TriggerProcessor to make its
purpose more clear. This requires the update of the map2.txt files.

Removed valid flag from Liquid and Trigger waveforms in Structure.cpp
and replaced it with multiplicity. Events with no valid pulses will
have a multiplicity of zero.

Removed Mike's analysis code from LiquidProcessor. Also removed the
short and long integral variables from the Liquid branch. Pulse
analysis will now be done externally.

Added new command line arguments to turn the saving of processor
waveforms on or off. Currently, trigger_wave, liquid_wave,
logic_wave, and vandle_wave are accepted. However, only Trigger and
Liquid have saving of waveforms implemented.

Added a new 'tools' directory with PulseViewer.cpp and
PulseAnalyzer.cpp. These may be compiled using the Makefile. i.e.
'make PulseAnalyzer' and 'make PulseViewer'.
Added configuration files

Added the ability to read RootPixieScan .config files. Config files
should be stored inside the config directory with the other files
which are used for configuration (map2.txt, cal.txt, etc). Config
files may be loaded by passing their filenames to Scanor. i.e.
./PixieLDF hist_name /path/to/file.config

Removed the ability to pass arguments through the command line, other
than the name of the config file to load. These options have been
moved to the configuration files.

Changed setup.cfg to a symbolic link named 'setup'. This link should
point to whichever config folder contains the files you wish to use.
The files contained in the config folder are (map2.txt, cal.txt, etc).

Removed PathHolder. Source files which load a specific file from the
config folder will now use the symbolic link 'source'.

Removed multiple files. LitePositionProcessor.cpp/hpp, ScintRoot.cpp/hpp,
RootProcessor.cpp/hpp, and GetArguments.hpp because they are not used.

Changed the Makefile to build only the object files necessary for
linking and running the program.

Did some general cleanup on some source files. Initialize, MapFile,
DetectorDriver, PositionProcessor, TimingInformation, TraceFilterer,
and TreeCorrelator. Fixed formatting mainly.
Modified PulseAnalyzer/Viewer

Changed PulseAnalyzer and PulseViewer to take changes to the root
output format into account. Both tools will now expect a vector
of ints named 'something_wave' and an unsigned int with the name
'something_wave_mult'. The root name (something) is passed from
the command line. The program will automatically determine the
pulse size from these two branches.

Method 3 and 4 use the energy of the pulse for plotting. This energy
is obtained from a vector of doubles named 'something_energy'. Method
3 and 4 will not be usable if the program cannot find a branch with
this name.