Adding Doxygen support. Run `make doc` in your build directory!
Some cool doxygen features: TODO list!
FIX format warning for scanf when reading config (bool vs int)
Error checking in GParticleReconstruction::OpenCutFile()

*) Throw false in case file can't be opened
*) Use GetObject() instread of Get(). Provides type checks then loading objects.
*) Throw false if object can't be found inf file
Doc for GParticleReconstruction::OpenCutFile()
Terminate program if a cut can't be loaded

This avoids silently not including some particles in the output
Tree production in physics class

Added first portion of tree production in physics class. This will be done ahead of histograms.
Improved tree handling in Pi0 physics class.

A two stage physics analysis is now implemented in the example PPi0 class. A basic tree is created containing only the calculated Missing Mass and Energy, along with the TC, incident photon energy, theta, phi and time for timing cuts. Histograms can be produced from this tree (at the same time) without interfering with the tree. This is done so that the histogram binning can be changed on the fly (as well as missing mass cuts and prompt/random timing cuts). All controls are still hard coded into the init section, however this will change to be user controlled (either via command line flags, or through a config file).
Changes to Charged-Neutral conditions (Particle reconstruct)

Setting up basic outline for improved "charged particle marking". This is a seperate parameter to full charged particle identification (ie dE_E cuts) which looks at the energy deposition in the charged particle detectors to mark a particle as charged. Due to experimental problems with individual detectors, this must be done in a way which is possible to completely ignore the information from an individual detector.
Updates to PEta class

Small updates to reflect changes in PPhysics class (HistFile for histograms to seperate from tree file)
Added check for treeRawEvent_clone before filling or writing it
Add build to gitignore
Adding file selection stuff
Got server section working, need to add loop for multiple entries in server file, made everything standard strings to clean up code
Added some message output
Fixed boolean return from File method
DataCheck handling (CB hole problem) and proper scaler storage

New additions to handle rejection of data due to missing CB sections (now a reasonably common data issue). Also, proper storage of scalers is now done. TraverseEntries - the original routine to step through data is replaced by a routine to step through the data scaler read by scaler read. If the data passes any data checks turned on, the events within a scaler read are analysed and the corresponding scaler read is stored.
Traverse Acqu Entries improved for MC data handling

Call to open Scaler tree will not fail GoAT running (this change is required to match current output from Acqu which does not produce the scaler tree for MC data). Routine to traverse entries is also renamed back to TraverseAcquEntries for consistancy.
File handling controls in PPi0

Small fixes for file handling in class PPi0.
Restructuring of folder structure!