Merge branch 'release/alcapana_prod_run_3'
Merge branch 'release/alcapana_prod_run_3.1'
JQ: Fixes #117
Merge branch 'hotfix/corrections_loaded'
Merge branch 'hotfix/corrections_loaded' into develop
Merge branch 'develop' of github.com:alcap-org/AlcapDAQ into develop
Modify doxygen config
Name the output directory as 'doxygen'
Make sure doxygen is a phony target for it to run
Add a .gitignore that will prevent doxygne output being committed
Merge branch 'feature/BK_doxygen_makefile' into develop

Allows makefile to generate doxygen as suggested in issue #126
Add further demonstration code into the skeleton tap generator script
Make sure that kDefaultConfig is used if no config is specified in
Generator ID constructor
Remove debug=all, label list_modules and add vim modeline
Break up loading of the modules file into 2 steps (load then make
modules separately).  Also added some extra options to control debugging
outputs
Added demonstrations of the new debug outputs to testModule.txt
Added doxygen comments for GetRunNumber in CommandLine.h
Created a SetupNavigator, which currently only handles the run number
but will in the future absorb TSetupData
Pass the command line options to the new SetupNavigator so the we can
obtain the run number from it.

Resolves issue #75 and the question in #119 of obtaining the run number
Added some extra commenting