Fall 2018 ver1 (#507)

* new Cher calib. coeffs. for HMS and SHMS

* fix def-file bugs

* comment out shms histograms not used in online monitoring

* comment out hms histograms not used in online monitoring

* Added back the DC efficiency plots

* Fix T3 in hms_stack.map

Modified hms_stack.map to put T3 in the right channel.

* Modify hdc_cuts.param and hdc_tzero_per_wire.param

1) Changed the per wire tzero offsets for the formerly bad  TDC
  since now that TDC module has it own reference time and tzero
  offsets for these channels match the other TDC modules.

2) Change the per plane tzero offsets by 50ns.

* add hT3 to htrig map

* add per wire dc eff to singles replay

* minor aesthetic changes

* remove line which was producing error

* remove creation of root file for monitoring histos

* clean up .gitignore

* update coin cuts and report file templates

* Kinematics files update

* Update parameter files for new time cuts and calibrations

* Correct replay_production_hms_coin_all.C

* Update pcal_calib.param

put back a old pcal_calib.param to replace a bad recent calibration.

* Commiting some of the calibrations and changes that have occured over our physics runs

* Modified onlineGUi ped_tracking.C and ped_tracking_trigger.C

Set the Y-axis of the pedestal difference plot to the minimum of 15
or 1.2 times the largest difference.

In ped_tracking
---------------
If both golden and current run do not have a pedestal for that channel,
then ped diff is zero.

If only the golden run does not have a pedestal for that channel , then
sets the ped difference to  negative pedestal value for the current run.

If only the current run does not have a pedestal for that channel , then
sets the ped difference to pedestal value for the golden run.

* Add onlineGUI/UTIL/GEN/flyeye_occupancy.C

Takes the 1D histogram of the shower block occupancy and makes
a 2D plot of occupancy for each row and column.

* Add histograms of the DC wiremaps for all DC hits.

Modified HMS/PRODUCTION/DC/hdc_histos.def and SHMS/PRODUCTION/DCpdc_histos.def to
have histograms of wiremaps for all hits in the DC.

Modified CONFIG/HMS/PRODUCTION/hms_coin_production.cfg and
CONFIG/SHMS/PRODUCTION/shms_coin_production.cfg to plt the histograms.

* Updated COIN/standard.kinematics

* Updated the aerogel calibrations and made some changes to the calibration script to make it easier to use

* Aerogel calibration was updated by Vladimir and I for new kinematics

* intermediate backup after hallc_replay file system restore

* Updated standard.kinematics with most recent runs at 6.495

* Updated version of standard.kinematics for first setting of Q2=5.5, W=3.02

* Update to standard.kinematics for luminosity and physics

* Updated versions of current calibrations for each luminosity run (5150-5168)

* Updated standard.kinematics for 9.53 SHMS angle

* BCM calibration updates for rest of luminosity runs

* Update to standard.kinematics for 9.555 angle change

* Updates to standard.kinematics for 6.5 deg setting change

* add bcm current files

* update hms cal calib and shms hgc timing cuts

* update kinematics file at end of kaon-lt running

* update submodules

* update kaonlt sub module after recen updates

* update kaon-lt submodule, yet again...

* remove bcm param files

* revert experiment specific changes