todo

 todo

make sure that all the variables are added to .proj as uppercase, and check that no files downstream in process rely on lowercase vars set in get_variables.

change and check variables in template_files.sh exist 

when external project settings file either custom or default is used that no variables are unset.

remove set -a etc from get_variables and make sure that all files that need vars source .proj

change all container run scripts to only source their variables from the local settings file, and perhaps the super_settings file.