* Modify protoroot file to point to symbollically linked latest file

* Correct pdc online GUI proto-root file name

* Minor changes to SHMS maps

* Minor changes to HMS maps

* Update merge list

* Update crate 3 map for coin

* Update coin maps

* Initial attempt at coincidence replay

* Update coin maps and replay script

* Update SHMS maps with FADC reference times

* Same for HMS

* Add FADC reference times to coin maps

* ignor nfs temp files

* Add SHMS FADC reference time signal

* Modify report files and templates to better quantify the deadtimes

* Push initial changes for Steve

* Include failed state of HMS scalers replay script

* Include proper(?) method for obtaining event 129 scaler reads

* Ensure that trigger apparatus cut file has similar flow to stack and production to avoid confusion

* Remove reference time which serves as a reference time for the trigger apparatus

* Update maps corresponding to previous commit

* Ignore # files

* Update test stand cuts file to match production and stack

* Update test stand cuts file to match production and stack on HMS side

* Add vim lint to .gitignore

* Update replay scripts to search in a list of paths

- NOTE: This requires the podd submodule be updated to include
  modifcations to the THaRun constructor that can search a pathList.

- The default './raw' and './cache' pathnames that are searched here
  should generally be symlinks to the relevant local path on the Hall C
  cluster, and the /cache/mss/hallc/.../raw/ path, respectively. For
  example:
    cd hallc_replay
    ln -s /net/cdaq/cdaql3data/coda/data/raw raw
    ln -s /cache/mss/hallc/spring17/raw      cache

- FWIW: The batch filtering of the replay scripts was done with
  this perl script:
    cd SCRIPTS/
    find . -name '*.C' -exec ./filter.pl {} \;
  --- filter.pl ---
  #!/usr/bin/perl

  use File::Slurp;

  my $file = read_file($ARGV[0]);

  $file =~ s/\Qchar RunFileName[100];\E\W*\Qsprintf(RunFileName, RunFileNamePattern, RunNumber);\E\W*\QTHaRun* run = new THaRun(RunFileName);\E/THaRun* run = new THaRun( pathList, Form(RunFileNamePattern, RunNumber) );/s;

  $file =~ s/\Qconst char* RunFileNamePattern = "\E.*?\/(.*?\.dat)";/const char* RunFileNamePattern = "$1";\n  vector<TString> pathList;\n    pathList.push_back(".");\n    pathList.push_back(".\/raw");\n    pathList.push_back(".\/cache");\n/s;

  write_file("$ARGV[0]", $file);
  ---

* Add ignore stuff

* Include TI trigger inputs into scalers

* Add TI trigger inputs to param files

* Add TI trigger inputs to trigger maps

* Add HMS trigger apparatus variables to trigger test stand

* Remove raster from trigger apparatus map

Update HMS maps to include new TI trigger inputs

* Remove fast raster from trigger apparatus map

* Add TI trigger inputs to SHMS maps

* Create separate DBASE directory for SHMS

* Create separate DBASE for SHMS

Fix plethora of issues in HMS replay scripts

* Do not delete onlineDict.h

* Ignor header file

* Fix typo in map file and get rid of debug statement

* Adapt shms scaler online GUI for new naming scheme

* Remove deprecated config files

Move scaler config files to own directory

* Fix scalers replay script so it does not seg fault

* Modify online GUI for HMS scalers to function with new naming scheme

* Auto-indent

* Move staggaling files to examples

* Add directory structure to online GUI

* Add summer 2017 software analysis workshop example

* Add summer 2017 software analysis workshop example for real this time

* May 26, 2017 -- Long overdue push, some old Calibration Scripts but also the presently working analysis and Calibration scripts in Final Scripts directory.

* Updated Calibration with pulseAmp script.

* root file

* added Rootfiles

* Rewrote pulseAmp analysis, works much better now.
Included Degtiarenko's code to evaluate as a better alternative.
Started the write up for the actual calibration process

* Updated Analysis scripts, started deciphering Fortran code.

* test

* TEST

* test

* bla

* blah

* boring git stuff

* git stuff

* Made the master branch much more organized/presentable

* Finializing directory. Modified how calibration appears/output the calibration constants

* Updated the analysis and visualization scripts for NGC.

* Version of Calibration suitable for the Summer presentation.

* Removed debugging line

hcal.param
   1) gains for run 303,
   2) hcal_AdcNegThreshold=0.
   3) hcal_AdcPosThreshold=0.

pcal.param
   1) gains for run 464
   2)pcal_AdcNegThreshold=0.
   3)pcal_AdcPosThreshold=0.
   4)pcal_arr_AdcThreshold=0.0

Modified DEF-files for new names for the Cherenkov and Aerogel

The heavy gas and noble gas signals were mislabled at the FADC.
Decided to change map and leave cables in place.

Made replay_hms_report.C which expands on replay_hms.C
Need to create REPORT_OUTPUT directory

new HMS Hodo timing offsets for 3/4 trigger
save old HMS Hodo timing for 4/4 trigger
new SHMS Hodo timing offsets for 3/4 trigger
Updated HMS and SHMS onlineGUI config and macros

+#*
+hcana
+raw