So if I understand this correctly, he's written a program that can mess with the contents of a file such that when you run the file contents through some hash function, the resulting hash is an encrypted message you generated with someone's public key. Then, the owner of the private key can try and decrypt the hash of the file to see if there's a message for them, effectively letting you hide an encrypted message covertly inside the file. It's very difficult to tell if the hash is an encrypted message, or if it's just a hash.

But how do they modify any type of file to generate the correct hash? A carefully designed hash function?