Generating checksums—cryptographic hashes such as MD5 or SHA-256 functions for files is hardly anything new and one of the most efficient means to ascertain the integrity of a file, or to check ...

If you're doing the MD5 check as part of copying the directory structure, then you can use rsync -c which will copy the files and compute/verify the MD5 hashes on the fly.

Any idea what purpose including an MD5 Sum file within a zip file that you're downloading serves? I understand the algorithmic checking to make sure the file hasn't been modified.