I think this will give you the best information, it links to the currently-implemented draft and lists divergences between that draft and Let’s Encrypt’s software (Boulder).
@jared.m is correct (Thanks!) - Boulder and the "V1" API evolved alongside the draft ACME protocol document. At the time of implementation none of the endpoints you mention existed We document each as a divergence and you'll find that the "V2" API we intend to make available in addition to V1 in Feb will have the endpoints you are mentioning and considerably fewer protocol divergences for clients to respect.
The first place we went was Documentation and then Client and Large Provider Integration Guide; unfortunately, we did not find any details there. From there, we went to Getting Started and found that you were using the acme protocol, but the link on that page didn’t take us to the details of the protocol. From there we went to the FAQ and found a link to ACMEv2, which is how we got there – this was the first link we found that actually took us to a specification, so that’s what we assumed was being used.
I would say that as a developer, the first place we’re going to go is the integration guide, and unfortunately, we didn’t find details on integration there. Additionally, the Getting Started page is another place that one would probably check first; if not the integration guide, and the details were not found there either. I think that the FAQ is also another good place to have links to the actual specification that you’re using.
I have to say it was a frustrating experience for a seasoned developer that’s just trying to get to the API details and some example code, there was not much to be found. It’s a very complex protocol which definitely needs to be clearly documented with some more details showing example communications between the client and server.
On that page, there are three hyperlinks to the actual protocol draft: a formatted and structured version of the current draft underneath the html hyperlink and also an unstructured one beneath the plain hyperlink.
By the way, the same hyperlink to the ACME protocol exists on the "Getting Started" page.
What "details of the protocol" were you unable to find on the protocol page?