Is there a documentation about the crypto-primitives and the crypto protocols, that are used by iota and how they are implemented? And if so, where ;-)
A good starting point is the IOTA Documentation:
As a next step you could look at the actual IOTA Reference Implementation (IRI) on GitHub:
For the theoretical framework behind all of this you should read:
Detailed documentation on the cryptography of IOTA can be found in the following page. There is a specific section on the streams in IOTA which is a recent cryptographic construction introduced by IOTA.