If it was just one thing or the other, perhaps he wouldn't have been so critical of it. People are going to understand if you require a few paths to be changed or some files to be downloaded manually into specific relative locations. The ask is only that somebody should be able to use the code without doing their own novel research, and be able to verify it's doing what it is claimed to be doing. If this means your download links need to point to the right location, the code has to run in a location other than /home/hellokitty/ml, and that it needs to meet standards of readability—well, good, that's what the scientific process is about.
