To think about:

Is it possible to reduce the repetition in path_names_ files?

For example, using mkmf to search directories rather than individual files.

It seems prone to error to change (for example) 91 path_names files when a new file is required for preprocess.

At least for preprocess, and other programs that the path names don't change between models, it seems like we could have one path_names_preprocess.

../../../build_templates/mkmf -v -p preprocess -t ../../../build_templates/mkmf.template   \   
 -a "../../.." path_names_preprocess 

becomes

../../../build_templates/mkmf -v -p preprocess -t ../../../build_templates/mkmf.template   \   
 -a "../../.." HELLO_ONE_LOCATION/path_names_preprocess