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Troubleshooting

If ./d-prep.sh doesn't work, try removing non-folders from GitHub.
Comment out ./attention_needed_bell.sh to #./attention_needed_bell.sh in big_medit.sh (sic) if playing the bell causes big_medit1.sh to hang.
Change "GitHub" to the new name of the GitHub folder in cat_arg_files.pl and cat_alg_files.pl.
Try running chmod 777 *.sh where *.sh is the name of a Shell script that won't run.