JG: simple script that checks features of trees from common runs.
Moved all files into the appropriate directory, to be summarized at a
later date on the elog.  The code is not expected to work as yet as the
Makefile will now need updating.
Updates to Makefile and files.make to handle the new directory
structure.  If new directories are added or renamed, change the
contents of src/files.make.
Removed old includes for some modules files which are no longer needed.
Added handling of missing ROOT setup script in the thisdaq.sh script
Removed ProcessCorrectionFile (to the deprecated code sub-directory)
and removed it's use from the main program.
Renamed utils.h to CommandLine.h and for .cpp.
Moved the CommandLine.* files into the framework sub-directory
Merge branch 'feature/AE_low_level_data_quality' into develop. AE: Joe's script that checks if ROOT files are the same needs to be added
Merge branch 'develop' of github.com:thnam/AlcapDAQ into develop
Merge branch 'feature/BK_tidy_rootana_src' into develop
This rearranges the source code of the src directory so that we can see
more clearly the purpose of each class, just from the directory
structure
Added an AppendToOption and renamed AddOption to SetOption for the
modules::options class
Add support for appending a value to an existing option.  This is still
untested at this point.
Parse a += operator to append to an existing option.  Stil untested at
this point
Debugged the implementation of the new config file += operator
Initiliase variables following valgrind warning
More comments and rearrange order of printing and option parsing
Change the list character from just whitespace to using a colon
Commiting unfinished work on MakeAnalysedPulses so I can change branch
and merge elsewhere to develop.  I don't expect things to work at thi
commit
Added a field to get the name of the detector to the base class for a TAP generator.
We can use this to inspect a generator for the detector that it is due
to analyse.