There are several flags in the Makefile that you can use to control the flow of the analysis. These include:

USEROOT - To use this flag, you must have installed the ROOT analysis package on your system and have the ROOTSYS, PATH, and LD_LIBRARY_PATH environment variables set correctly (according to the ROOT installation). This flag compiles in the ability to output a .root file depending on a set of conditions in the RootProcessor but otherwise does not affect the functioning of the code.
CXXFLAGS += -DVERBOSE - This defines the VERBOSE preprocessor condition. Turn this on in order to have a wickedly verbose scan.
ONLINE - This will create a much quieter scan code. Outputting to the terminal takes time, and you don't always want that when running.
DEBUG - This will enable verbose debugging for the TreeCorrelator. It will be useful if there's something that's going wrong.
PULSEFIT - This includes the libraries for GSL necessary for the high resolution timing.
GGATES - Defines gamma gates for the GeProcessor. This turns on Gamma-Gamma angular distribution and Gamma-Gamma-Gamma gates.