TreeManager: Changed branch names to not include special chars like "+" or "-"

These chars make it impossible to access the trees with TTree::Draw().
GTreeParticle: removed the "." at the end of the "particles" branch name
Changing RawEvent to RawParticle, and adjusting the variable names of those branches to reflect new ones
Merge branch 'development' into NewBranchNames

Conflicts:
	CMakeLists.txt
Changed remaining RawEvent occurances in ParticleReconstruction, after merging the version after having added TOF in
Finished changing branch names and their corresponding variable names and getters, to reflect new namings for RawParticle tree
Changed branch names, corresponding variable names, and getters, to reflect new namings for Tagger tree
Changed branch names, corresponding variable names, and getters, to reflect new namings for LinPol tree
Changed branch names, corresponding variable names, and getters, to reflect new namings for DetectorHits tree
Changed branch names, corresponding variable names, and getters, to reflect new namings for Trigger tree
Changed branch names, corresponding variable names, and getters, to reflect new namings for Scaler tree
Changed branch names, corresponding variable names, and getters, to reflect new namings for EventParameters tree
Fixed some output messages, no real code changes
Fixed a typo in GTreeA2Geant
Moved the command line parsing and base config file parsing into GConfigFile, allowing the main.cc files to be cleaned up significantly.
Changed default prefix handling a little bit, since otherwise physics classes defaulted to the same prefixes as GoAT when using GConfigFile for the base configuration
Removed extra text from Init error message
Removed duplicate entries for some GoAT inclusions
Starting my own pi0 class
Personal config choices