LLVM / Clang system config file setting breaks with -no-canonical-prefixes

[chandlerc]

brew gist-logs <formula> link OR brew config AND brew doctor output

> brew config
HOMEBREW_VERSION: 4.4.31
ORIGIN: https://github.com/Homebrew/brew
HEAD: 0046519c08cd3967e0934c82195361ac7e76c567
Last commit: 5 days ago
Branch: stable
Core tap JSON: 19 Apr 21:14 UTC
Core cask tap JSON: 19 Apr 21:14 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: nvim
HOMEBREW_MAKE_JOBS: 10
Homebrew Ruby: 3.3.8 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.3.8/bin/ruby
CPU: deca-core 64-bit arm_firestorm_icestorm
Clang: 16.0.0 build 1600
Git: 2.39.5 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 15.4-arm64
CLT: 16.3.0.0.1.1742442376
Xcode: 16.2
Rosetta 2: false

> brew doctor
Your system is ready to brew.

Verification

• My brew doctor output says Your system is ready to brew. and am still able to reproduce my issue.
• I ran brew update and am still able to reproduce my issue.
• I have resolved all warnings from brew doctor and that did not fix my problem.
• I searched for recent similar issues at https://github.com/Homebrew/homebrew-core/issues?q=is%3Aissue and found no duplicates.

What were you trying to do (and why)?

Use clang with the flag -no-canonical-prefixes, which results in generally better paths by preserving useful symlinks, and has worked for many years.

What happened (include all command output)?

> echo "int main() {}" | clang -c -o test.o -x c -

> clang -o test test.o -v
Homebrew clang version 20.1.3
Target: arm64-apple-darwin24.4.0
Thread model: posix
InstalledDir: /opt/homebrew/Cellar/llvm/20.1.3/bin
Configuration file: /opt/homebrew/etc/clang/arm64-apple-darwin24.cfg
System configuration file directory: /opt/homebrew/etc/clang
User configuration file directory: /Users/chandlerc/.config/clang
 "/usr/bin/ld" -demangle -lto_library /opt/homebrew/Cellar/llvm/20.1.3/lib/libLTO.dylib -dynamic -arch arm64 -platform_version macos 15.0.0 15.4 -syslibroot /Library/Developer/CommandLineTools/SDKs/MacOSX15.sdk -mllvm -enable-linkonceodr-outlining -o test test.o -lSystem /opt/homebrew/Cellar/llvm/20.1.3/lib/clang/20/lib/darwin/libclang_rt.osx.a

> clang -no-canonical-prefixes -o test test.o -v
Homebrew clang version 20.1.3
Target: arm64-apple-darwin24.4.0
Thread model: posix
InstalledDir: /opt/homebrew/opt/llvm/bin
System configuration file directory: /opt/etc/clang
User configuration file directory: /Users/chandlerc/.config/clang
 "/usr/bin/ld" -demangle -lto_library /opt/homebrew/opt/llvm/lib/libLTO.dylib -dynamic -arch arm64 -platform_version macos 15.0.0 15.0.0 -mllvm -enable-linkonceodr-outlining -o test test.o -lSystem /opt/homebrew/opt/llvm/lib/clang/20/lib/darwin/libclang_rt.osx.a
ld: library 'System' not found
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Note that in the failing execution the system configuration file directory becomes /opt/etc/clang instead of /opt/homebrew/etc/clang. The result is that it fails to find the configuration file and include the relevant SDK paths.

What did you expect to happen?

Both clang invocations should find the configuration directory and succeed.

Step-by-step reproduction instructions (by running brew commands)

The above should be a complete sequence of steps to reproduce. Requires having `llvm` installed.

[daeho-ro]

homebrew clang binary is linked,

/opt/homebrew/opt/llvm/clang -> /opt/homebrew/opt/../Cellar/llvm/20.1.3/bin/clang

and config path is defined by relatively.

clang_config_file_dir.relative_path_from(bin)

---

When the path is simplified,

bin: /opt/homebrew/Cellar/llvm/20.1.3/bin
config: /opt/homebrew/etc/clang

clang_config_file_dir.relative_path_from(bin) = ../../../etc/clang

and -no-canonical-prefixes added,

bin: /opt/homebrew/opt/llvm
config: /opt/homebrew/opt/llvm/../../../etc/clang = /opt/etc/clang

the config path is now wrong.

[chandlerc]

I'd suggest laying out the configuration etc directory as a sibling to the bin directory, and making the path of ../etc/clang work in both cases by symlinking /opt/homebrew/etc/clang to /opt/homebrew/opt/../Cellar/llvm/20.1.3/etc/clang parallel to the binary symlink.