Improve documentation

[Nashtare]

In the line of #19, it would be beneficial to strengthen the documentation of the codebase, in particular on the protocol-decoder subcrate side, to allow both maintainers and external contributors an easier time when diving into the internals of proof IR generation.

Similarly to what was done in 0xPolygonZero/plonky-block-proof-gen#8, it may be nice to add sufficient meaningful documentation so that we can add

#![cfg_attr(docsrs, feature(doc_cfg))]
#![deny(rustdoc::broken_intra_doc_links)]
#![deny(missing_docs)]

at the top of the protocol-decoder crate without compilation error.

Probably not of highest priority for now, but adding a tracking ticket nonetheless.

Side note: The attributes above were added as part of 0xPolygonZero/plonky-block-proof-gen#8 but were removed during the merging with this repo. It could be re-enabled for the plonky-block-proof-gen subcrate when dealing with this issue, as the requirements are already satisfied.