Homebrew cleans metafiles after formula installation even if `skip_clean` is used

[botantony]

brew doctor output

Your system is ready to brew.

Verification

• I ran brew update twice and am still able to reproduce my issue.
• My "brew doctor output" above says Your system is ready to brew or a definitely unrelated Tier message.
• This issue's title and/or description do not reference a single formula e.g. brew install wget. If they do, open an issue at https://github.com/Homebrew/homebrew-core/issues/new/choose instead.

brew config output

HOMEBREW_VERSION: 4.6.18-19-g14304c5
ORIGIN: https://github.com/Homebrew/brew
HEAD: 14304c59de7c70837e4b7a1245ced40e30ae8c4b
Last commit: 3 hours ago
Branch: main
Core tap HEAD: baae9195727a811137d1bc0dc62fc0da5675119c
Core tap last commit: 13 minutes ago
Core tap JSON: 21 Oct 21:17 UTC
Core cask tap HEAD: e1ec6c6c2925dc9beaba6a4ca74cf6ea11f74fe0
Core cask tap last commit: 70 minutes ago
Core cask tap JSON: 21 Oct 21:17 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.SPqv1guT2P/org.xquartz:0
HOMEBREW_EDITOR: nvim
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 8
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 3.4.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.4.5/bin/ruby
CPU: octa-core 64-bit arm_blizzard_avalanche
Clang: 17.0.0 build 1700
Git: 2.51.1 => /opt/homebrew/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.0.1-arm64
CLT: 26.0.0.0.1.1757719676
Xcode: 26.0.1
Rosetta 2: false

What were you trying to do (and why)?

A user wanted to install changelog.md files to libexec as the program uses this info to determine the version

Related to Homebrew/homebrew-core#249984

What happened (include all command output)?

Adding skip_cleanup "libexec/changelog.md" didn't work, so they had to create a symlink in post_install block

What did you expect to happen?

Do not remove this file

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

# Add something like `skip_clean "libexec/README.md»` and `libexec.install "README.md"` to any formula
brew install --build-from-source <formula-name>
# You can observe that this file is installed while the program compiles
# but after `Cleanup` it disappears

[aboodic]

Add something like skip_clean "libexec/README.md» and libexec.install "README.md" to any formula

brew install --build-from-source

You can observe that this file is installed while the program compiles

but after Cleanup it disappears

[cho-m]

To be precise, Homebrew performs metafile moving before cleanup phase so skip_clean has no impact.

brew/Library/Homebrew/build.rb

Lines 208 to 210 in 103917b

	# Find and link metafiles
	formula.prefix.install_metafiles T.must(formula.buildpath)
	formula.prefix.install_metafiles formula.libexec if formula.libexec.exist?

I am guessing metafiles were moved to use a consistent location for formulae that install entirely into libexec (e.g. Java formulae).

The code for this is pretty old now. May be worth considering if this is still the best way of handling.

Maybe we should consider symlinking to prefix instead.