llvmPackages.clang-tools: add support for -cxx-isystem

[reckenrode]

This is necessary after #445095, which moved libc++ to -cxx-isystem to improve compatibility with build systems that invoke clang to compile C++ code.

Things done

• Built on platform:
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• Tested, as applicable:
  • NixOS tests in nixos/tests.
  • Package tests at passthru.tests.
  • Tests in lib/tests or pkgs/test for functions and "core" functionality.
• Ran nixpkgs-review on this PR. See nixpkgs-review usage.
• Tested basic functionality of all binary files, usually in ./result/bin/.
• Nixpkgs Release Notes
  • Package update: when the change is major or breaking.
• NixOS Release Notes
  • Module addition: when adding a new NixOS module.
  • Module update: when the change is significant.
• Fits CONTRIBUTING.md, pkgs/README.md, maintainers/README.md and other READMEs.

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[reckenrode]

Targeting to staging due to the number of rebuilds.

[mattkang]

I think something about this may have broken my environment. I actually do not use clang but rather gcc. Was using clang-tools merely for clangd as an LSP. Any idea why this might be happening and how I can fix it?

[reckenrode]

What branch are you using? This fix won’t land in master until after the next staging cycle. If you’re using the release-25.11 branch, it won’t land until after the next staging-25.11 cycle. From what I understand, a (likely final) staging-25.05 cycle is planned next, so it may take a little bit for the backported fix to hand in 25.11.

[mattkang]

@reckenrode On nixos-unstable. Double-checked before posting and now triple-checking... pretty sure I've got it. Actually now I'm second-guessing

EDIT: you're right @reckenrode don't have it yet. Hopefully this PR fixes my issue. Will keep my eyes peeled.

[HuaHuaY]

I use official nixos-unstable and clangd can't find the header files in the standard library.
I fork nixpkgs, cherry-pick this commit to my repo, add the repo into flake's input section and use clang-tools in the repo. Clangd works well. Thanks for your fix.
@mattkang FYI

[GrahamDennis]

Does this PR Does this PR need to land on master?

[reckenrode]

It’s currently going through staging-next.

https://nixpkgs-tracker.ocfox.me/?pr=462747

[hzeller]

Since this is a crucial component to have clangd work, unchanged unstable and master are not very usable for weeks now to do c++ development. So (at least for me), it is a somewhat critical problem that can be fixed with an unlikely-to-cause-trouble patch.
Would it be possible to cherrypick this change to master, or would that mess up the merge cycle ?

[reckenrode]

It has to go through staging due to the number of rebuilds it would cause.

If you really need the fix, you can try using the staging-next branch. Note that some of the packages you use may not have been built yet.

[mattkang]

I just want to second that this has made unstable unusable for me. This is required for any real C++ dev. How much longer until it hits master?

[hzeller]

for my personal projects, I created an overlay, putting that in a file in ~/.config/nixpkgs/overlays/clang-tools-patch.nix

with content

# Locally applying PR 462747, which modifies the wrapper, that ends up named
# clangd in the final package. So patch that `clangd` script with that change.
# The patch contains a path to the wrapper, but we apply it directly to the
# clangd script where it ends up in.
##

# Define a transformation, then apply it to all llvm versions of interest.
final: prev:
let
  # Transformations for each version
  patchClangTools = llvmPkgSet: llvmPkgSet.overrideScope (lfinal: lprev: {
    clang-tools = lprev.clang-tools.overrideAttrs (oldAttrs: {
      postInstall = (oldAttrs.postInstall or "") + ''
        echo "Applying PR 462747 patch to the generated clangd wrapper..."
        patch -i ${prev.fetchpatch {
          url = "https://github.com/NixOS/nixpkgs/pull/462747.diff";
          hash = "sha256-WDP/WJAflkYw8YQDgXK3q9G7/Z6BXTu7QpNGAKjO3co=";
        }} $out/bin/clangd
      '';
    });
  });

  # ... all the llvm version we'd like to apply this to
  llvm_versions = [ "17" "18" "19" "20" "21" ];

in
prev.lib.genAttrs (map (v: "llvmPackages_${v}") llvm_versions) (name: 
  patchClangTools prev.${name}
)

nix-shell will look in that directory and apply overlays found.

So using clang-tools now nix-shell -p llvmPackages_21.clang-tools will use the patched version.

[Mic92]

Also now added in master #475078
Is a 25.11 backport needed?

[evysgarden]

A backport to 25.11 would be very appreciated since clangd is unusable for cpp on 25.11 otherwise

[nixos-discourse]

This pull request has been mentioned on NixOS Discourse. There might be relevant details there:

https://discourse.nixos.org/t/clang-clang-and-clangd-cant-find-headers-even-with-compile-commands-json/54657/13

[reckenrode]

The backport PR was #462884. The fix should already be in release-25.11.