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Running `make -C doc` to build the manual locally leaves .xml artifacts in the tree. These are ignored by git, but they still get included in the build when not using flakes, which causes the corresponding chapters not to be built.
Nixpkgs/doc
This directory houses the sources files for the Nixpkgs manual.
You can find the rendered documentation for Nixpkgs unstable on nixos.org.
Docs for Nixpkgs stable are also available.
If you want to contribute to the documentation, here's how to do it.
If you're only getting started with Nix, go to nixos.org/learn.