* Fix typo in HMS production cuts

* Corrected EDTM cuts and adjusted HMS TDC reference time cut to improve hodoscope efficiencies

* Fix bug for BCM cut currents in template files

* Add new BCM gains and offsets

* Update kinematics files

* Updated the kinematics files to be up-to-date. Note that the files had not been updated through the last two shifts (now fixed).

* updated kinematics files

* kinematics file from night shift

* Updated kinematics file, corrected mistake in HMS momentum that snuck in during OWL

* Kinematics files up to run 1799/2713 (HMS/SHMS)

* Include focal plane quantites in the tree

* Update kinematics files

* Updated kinematics files

* Update kinematics files

* Update submodules

Added setup_Directory() method to main_calib.C :: Added README for DC Calibration :: changed directory named from shms_dc_calib to dc_calib (#424)

* added HMS/SHMS DC Calib README :: changed directory name from shms_dc_calib to dc_calib

* added setup_Directpry() method in main_calib.C

* added optional flag to require single hit per event per plane for calibration :: re-define cuts for pid_hadron/pid_elec flags

* changed calorimeter leaf from X.cal.etotnorm to X.cal.etot

* added capability to created HMS/SHMS DC Calib Log directories to store the calibration information produced by the calibration script

* clean-up of SHMS DC Calibration Dir

* Added functionality to loop over Max number of entries, if user enters entries exceeding this maximum :: Add calorimeter etot_norm cut for beackground cleanup

* DC Calib: added option to only perform ONLY EL-CLEAN trigger cut, which reduces the background events in the chambers

* added the requirement for each event to a ONLY 1 hit, by requiring ndata==1. This way, background produced from multiple hits can be reduced.

* 1). Set 'hdrift1stbin' parameter by +1 ns offset, to improve the drift distances. 2). Added variable 't_zero_final' which includes the tdc offsets (from HMS ONLY), as opposed to only including the tzero value. This is used in the LookUpTable method() 3). Remove 0.5 ns offset from the min/max time, which puts integer drift time values at the edge of a given bin 4). Reduced total number of bins in which the drift time integration is done from 274 ns to 189 ns, since it was determined (from a conversation with Mark Jones), that drift times beyond this value had no contribution to the drift distance.

added optional pid_hadron cut in DC calibration :: changed 'good drift time fit' criteria to also consider fit slope of >0.2, based on previous observations of bad fits (#420)

2. Added capability for HMS/SHMS to calibrate using PID cuts on cerenkon/el clean trigger

Updated to match updated HCANA

Updated hcana code to have adcTimeWindowMin and Max
  for each Cerenkvo PMT so need to modify the
  adcTimeWindowMin and Max parameters to be an array.
  Keep them at -1000 and 1000 ns .

This adcTimeWindow is used to select which hit in the
 multihit ADC channel is pick as the "good" hit to
 us the later analysis.

Add branch=master to UTIL_ED

1) Applied weighted averages to edge wires
2) Added TDC offset correction to some of the 16-groups for HMS DC
3) Started Integration range at -20 ns for LookUp Table

* Fix bug in cuts file to ensure no decoding of EDTM events

* Update submodules

* Update kinematics files

Updated pxloscin,pxhiscin,pyloscin and pyhiscin for
the track efficiency tests.

Add file PARAM/SHMS/GEN/p_reftime_cut.param

Add file PARAM/HMS/GEN/h_reftime_cut.param

Update the COIN/SHMS/HMS general.param in DBASE
to use these files.

* Add utility submodules

* Remove UTIL directories since they are now submodules

* Simplification of hallc-replay to specifically support hallc-online hallc_replay operations.

* Re-add bcm_current_calib files

* Updates to CT kinematics file and macro

* Add utilities directory

* Move shell scripts into utilities directory and symbolicaly link them in the top level directory

Add recon matrix from COSY with Q2 at 20% higher for
 the defocussed run.

When using need to modify the pcana.param file
and uncomment DATFILES/shms-2011-26cm-monte_q2_p20_rec.dat
and comment out DATFILES/SHMS_fr3_rec__order_5.dat

* Include select PID & golden track leaves to quick replay ROOT files -Eric

* Update COIN kinematics file

* Update template files

* Updates to kinematics DB

In THcDC.cxx the method EfficiencyPerWire is called
which for the Golden track calculates which wire in each plane
"should" have been hit ( fills wirenumber in H.dc.wireHitShould[planenum]
and also calculates which wire "did" get hit by the track ( fills
wirenumber in H.dc.wireHitDid[planenum]) .

As an example of HMS histograms was created in
DEF-files/HMS/PRODUCTION/DC/hdc_eff_histos.def
which creates two sets of histograms for each plane
of the "should" and "did" wire numbers.

Updated hstackana_production.def to include
hdc_eff_histos.def and a newly created TEST_STANDS/DC/hdc_resid.def

For onlineGUI create UTIL/GEN/dcwire_efficiency.C for taking
ratio of the "did" and "should" histograms
and as exmaple HMS/TEST_STANDS/DC/hdc_wireeff.cfg for plotting
the histograms.

* Remove ROOT file

* Utilize #include directives in SHMS

* Update SHMS replay scripts accordingly

* Remove trailing white space

* Do the same for the HMS

* Replecate changes for coincidence replays

* Implement #include cut files correctly

* Update CT monitoring script

made new files for HMS/SHMS Coarsetracking and reconstruction
sections that were cut out of the hstackana and pstackana.
Then include them separately.

Move the Goldentrack to go after the ExtTarCor,
sinc ExtTarCor modifies the target quantities.