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I've researched some more candidates that could be considered an educational codebase.

Rob Flaherty has made a annotated version of jQuery version 1.6.2. This was created using a tool called docco by Jeremy Ashkenas. Jeremy himself also created CoffeeScript, as well as the backbone.js framework and the underscore.js library and as if that would not be enough already, he also made annotated versions of the latter two (underscore.js / backbone.js) that might be worth checking out as subject of study.

I think this approach lends itself well to (mostly) feature-complete and stable libraries. Having a rough order-of-magnitude how complex a codebase can be so that it could be broken down in that manner is also helpful to identify more candidates that could be annotated externally (as in: not necessarily by the original author as in the exceptional case of backbone and underscore).

One example external annontations of a codebase is Decoded: GNU coreutils by MaiZure. This is more a high-level guide into reading the implementations, than a line-by-line breaks down, which demonstrates also that there is a balance to be struck when one wants to teach about codebases that are well beyond the complexity of just snippets. MaiZure has multiple other projects of a similar nature.