Amusing development in the story, I wrote to ncbi asking why that folder is there, 4 days later I got the following response:
Thank you for the report. I do not see a directory called ProdigalHack in https://ftp.ncbi.nlm.nih.gov/genomes/ Maybe we removed it? I have not heard of a problem like this. Write back if you are still seeing it there.
Sure enough, that folder is not there anymore...
This https://github.com/hyattpd/Prodigal ?