[Halld-offline] New features checked into sim-recon

[Paul Mattione]

1) Users can now place custom cuts to pre-select which charged tracks and neutral showers they want to use for making the particle combinations.  This is done by creating new factories (with unique tags) for DChargedTrack and DNeutralShower in your plugin.  Instructions are at: 

https://halldweb1.jlab.org/wiki/index.php/Analysis_DReaction#Custom_Track_.2F_Shower_Pre-selection

2) Two new factories for DMCThrown have been added: tag = "FinalState" and "Decaying".  The "FinalState" factory will return the thrown particles that are in the final state, filtering out all of the various intermediate decaying particles, decay products of the final-state pions, and orphan particles.  The "Decaying" factory will return all of the decaying particles with PIDs defined in include/particleType.h (excluding any final-state particles that might decay).  Note that pi0's are listed in the "Decaying" factory since they are not detected.  Also note that resonances decayed by genr8 are not included in the genr8 output, and thus are not included in DMCThrown to begin with.  

3) You can now save TTrees containing only the thrown track data.  This is useful for saving the generated kinematics for calculating the acceptance.  Also, the interface for creating and saving TTrees has changed again.  This was done to not only accommodate thrown trees, but also to decouple tree creation from tree saving.  New instructions can be found at: 

https://halldweb1.jlab.org/wiki/index.php/Analysis_TTreeFormat#Create_TTrees

4) The danarest plugin now builds automatically when calling "make" in sim-recon/src/; before you had to go into the plugin folder and compile it yourself.  

5) In DAnalysisAction's, the Initialize() method has been decoupled from the function-call operator (execution).  This is so that the action is initialized (e.g. histograms created) even if it is never executed (e.g. histograms filled) (so that ROOT file merging works properly).  For actions added to a DReaction no change is needed, but other actions need to have the Initialize() method called manually.  For details:

https://halldweb1.jlab.org/wiki/index.php/Analysis_Actions#Setup_and_Execution

 - Paul