Incorrect LLVM system config directory when using clang-scan-deps

[tcbrindle]

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

brew config:

HOMEBREW_VERSION: 4.4.32-77-g9eb0357
ORIGIN: https://github.com/Homebrew/brew
HEAD: 9eb0357716192fc4273613220ef0ee700d213c40
Last commit: 8 hours ago
Branch: master
Core tap HEAD: 6c2620ecb4d741efbff32295f0c2ef01ebd5dfca
Core tap last commit: 10 hours ago
Core tap JSON: 28 Apr 17:03 UTC
Core cask tap HEAD: ba3da943abc861c24d078b63560419d6981c4f32
Core cask tap last commit: 11 hours ago
Core cask tap JSON: 28 Apr 17:03 UTC
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.d9VT5wDudZ/org.xquartz:0
HOMEBREW_MAKE_JOBS: 8
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 3.4.3 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.3/bin/ruby
CPU: octa-core 64-bit kabylake
Clang: 17.0.0 build 1700
Git: 2.49.0 => /usr/local/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 15.4.1-x86_64
CLT: 16.3.0.0.1.1742442376
Xcode: 16.3

Brew Doctor:

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected dylibs:
  /usr/local/lib/libarena-4e7c5e5c.dylib
  /usr/local/lib/libflate-4e7c5e5c.dylib
  /usr/local/lib/libfmt_macros-4e7c5e5c.dylib
  /usr/local/lib/libgetopts-4e7c5e5c.dylib
  /usr/local/lib/libgraphviz-4e7c5e5c.dylib
  /usr/local/lib/liblog-4e7c5e5c.dylib
  /usr/local/lib/libodb-2.5.0-b.13.dylib
  /usr/local/lib/libodb-2.5.0-b.5.dylib
  /usr/local/lib/libodb-sqlite-2.5.0-b.13.dylib
  /usr/local/lib/libodb-sqlite-2.5.0-b.5.dylib
  /usr/local/lib/librbml-4e7c5e5c.dylib
  /usr/local/lib/libregex-4e7c5e5c.dylib
  /usr/local/lib/librustc-4e7c5e5c.dylib
  /usr/local/lib/librustc_back-4e7c5e5c.dylib
  /usr/local/lib/librustc_borrowck-4e7c5e5c.dylib
  /usr/local/lib/librustc_driver-4e7c5e5c.dylib
  /usr/local/lib/librustc_llvm-4e7c5e5c.dylib
  /usr/local/lib/librustc_resolve-4e7c5e5c.dylib
  /usr/local/lib/librustc_trans-4e7c5e5c.dylib
  /usr/local/lib/librustc_typeck-4e7c5e5c.dylib
  /usr/local/lib/librustdoc-4e7c5e5c.dylib
  /usr/local/lib/libserialize-4e7c5e5c.dylib
  /usr/local/lib/libstd-4e7c5e5c.dylib
  /usr/local/lib/libsyntax-4e7c5e5c.dylib
  /usr/local/lib/libterm-4e7c5e5c.dylib
  /usr/local/lib/libtest-4e7c5e5c.dylib

Warning: Homebrew's "sbin" was not found in your PATH but you have installed
formulae that put executables in /usr/local/sbin.
Consider setting your PATH for example like so:
  echo 'export PATH="/usr/local/sbin:$PATH"' >> /Users/tristan/.bash_profile

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 Homebrew-built clang-scan-deps (from the LLVM package) to scan the module dependencies of a C++ file

What happened (include all command output)?

test_file.cpp:

#include <vector>

int main() {}

Command line

/usr/local/opt/llvm/bin/clang-scan-deps -- /usr/local/opt/llvm/bin/clang++ test-file.cpp -o test-file -v

Output:

Homebrew clang version 20.1.3
Target: x86_64-apple-darwin24.4.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
System configuration file directory: /usr/etc/clang
User configuration file directory: /Users/tristan/.config/clang
Homebrew clang version 20.1.3
Target: x86_64-apple-darwin24.4.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
System configuration file directory: /usr/etc/clang
User configuration file directory: /Users/tristan/.config/clang
clang -cc1 version 20.1.3 based upon LLVM 20.1.3 default target x86_64-apple-darwin24.4.0
ignoring nonexistent directory "/usr/include"
ignoring nonexistent directory "/System/Library/SubFrameworks"
#include "..." search starts here:
#include <...> search starts here:
 /usr/local/opt/llvm/bin/../include/c++/v1
 /usr/local/include
 /usr/local/opt/llvm/lib/clang/20/include
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
End of search list.
Error while scanning dependencies for test-file.cpp:
In file included from test-file.cpp:2:
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/vector:352:
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/algorithm:1854:
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/__algorithm/for_each.h:16:
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/__ranges/movable_box.h:21:
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/optional:1296:
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/atomic:607:
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/__atomic/atomic_flag.h:19:
In file included from /usr/local/opt/llvm/bin/../include/c++/v1/__thread/support.h:112:
/usr/local/opt/llvm/bin/../include/c++/v1/__thread/support/pthread.h:18:10: error: 'pthread.h' file not found with <angled> include; use "quotes" instead
/usr/local/opt/llvm/bin/../include/c++/v1/__thread/support/pthread.h:19:10: fatal error: 'sched.h' file not found

Note the "System configuration file directory" is set to /usr/etc/clang, which does not exist on my system -- it should be /usr/local/etc/clang for the Homebrew-provided config files

A workaround is to pass the correct directory explicitly using the --config-system-dir parameter:

/usr/local/opt/llvm/bin/clang-scan-deps -- /usr/local/opt/llvm/bin/clang++ test-file.cpp -o test-file --config-system-dir=/usr/local/etc/clang

What did you expect to happen?

clang-scan-deps would correctly report the dependencies of the C++ file

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

brew install llvm

then as above

[tcbrindle]

Possibly related to #220757