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Cyberbeing said:
If someone will either make a renaming batch file or torrent an updated site rip at some point I would be very thankful.
A Python script is fine too?
http://orphelin.no-ip.org/md5totags.py

When you run the script it asks for a folder. It searches that folder for images with md5 names, does an md5 search on imouto for those images, finds the new filenames, puts the old and new names in rename.txt and opens it for you so you can check if everything's fine and fix things that aren't before renaming.
It should only mess up if there are Japanese characters in a tag. They look fine in rename.txt but not in the actual filename after renaming (戦女神ZERO becomes 戦女神ZERO), you'll have to manually fix that.

Let me know if there are any problems.