A true gem is hidden down at the end of the first page:

https://github.com/fabiensanglard/chocolate_duke3D

[...] a port of the Vanilla source code with two goals in mind:

    Education: Easy to read/understand and very portable.
    Fidelity: The gaming experience should be similar to what ran in 1996 on our 486s.

And from the README:

    Aimed at education: A lot of comments and documentation has been added in order to help programmers to understand and learn.