HQTP v.2: Holy Quran Transfer Protocol version 2 [pdf]

I don't understand why they need to invent a protocol specific to the Quran.

I have seen before people develop markup languages specifically designed for the Christian Bible; this page has links to a few of them: http://ebible.org/usfx/Bible-encoding.htm

So, I could see the need for a markup language specifically for use with the Quran. But an entire application layer protocol seems like overkill, why not just use HTTPS?

Their protocol includes roll-their-own-security using SHA-1 and DSA. Much more advisable to just adopt TLS and use one of the existing widespread implementations of it, then they can easily adopt some much stronger algorithms than SHA-1 and DSS.