bundle/commands/cleanup: correctly handle .keepme references.

Extract the relevant logic from `formula.rb`, moving to `keg.rb` and
then use this logic in `bundle/commands/cleanup.rb` to ensure that we
don't say we need to uninstall formulae that should be still kept.

Library/Homebrew/bundle/commands/cleanup.rb

@@ -106,6 +106,13 @@ module Homebrew
           current_formulae.reject! do |f|
             Homebrew::Bundle::BrewInstaller.formula_in_array?(f[:full_name], kept_formulae)
           end
+
+          # Don't try to uninstall formulae with keepme references
+          current_formulae.reject! do |f|
+            Formula[f[:full_name]].installed_kegs.any? do |keg|
+              keg.keepme_refs.present?
+            end
+          end
           current_formulae.map { |f| f[:full_name] }
         end
 

Library/Homebrew/formula.rb

@@ -3146,8 +3146,7 @@ class Formula
             opoo "Skipping (old) #{keg} due to it being linked" unless quiet
           elsif pinned? && keg == Keg.new(@pin.path.resolved_path)
             opoo "Skipping (old) #{keg} due to it being pinned" unless quiet
-          elsif (keepme = keg/".keepme") && keepme.exist? && keepme.readable? &&
+          elsif (keepme_refs = keg.keepme_refs.presence)
-                (keepme_refs = keepme.readlines.map(&:strip).select { |ref| Pathname(ref).exist? }.presence)
             opoo "Skipping #{keg} as it is needed by #{keepme_refs.join(", ")}" unless quiet
           else
             eligible_for_cleanup << keg

Library/Homebrew/keg.rb

@@ -95,6 +95,8 @@ class Keg
   PYC_EXTENSIONS = %w[.pyc .pyo].freeze
   LIBTOOL_EXTENSIONS = %w[.la .lai].freeze
 
+  KEEPME_FILE = ".keepme"
+
   # @param path if this is a file in a keg, returns the containing {Keg} object.
   def self.for(path)
     original_path = path
@@ -592,6 +594,14 @@ class Keg
     end
   end
 
+  sig { returns(T::Array[String]) }
+  def keepme_refs
+    keepme = path/KEEPME_FILE
+    return [] if !keepme.exist? || !keepme.readable?
+
+    keepme.readlines.select { |ref| File.exist?(ref.strip) }
+  end
+
   def binary_executable_or_library_files
     []
   end

Library/Homebrew/test/bundle/commands/cleanup_spec.rb

@@ -44,7 +44,7 @@ RSpec.describe Homebrew::Bundle::Commands::Cleanup do
 
     it "computes which formulae to uninstall" do
       dependencies_arrays_hash = { dependencies: [], build_dependencies: [] }
-      allow(Homebrew::Bundle::BrewDumper).to receive(:formulae).and_return [
+      formulae_hash = [
         { name: "a2", full_name: "a2", aliases: ["a"], dependencies: ["d"] },
         { name: "c", full_name: "c" },
         { name: "d", full_name: "homebrew/tap/d", aliases: ["d2"] },
@@ -70,6 +70,17 @@ RSpec.describe Homebrew::Bundle::Commands::Cleanup do
         { name: "builddependency2", full_name: "builddependency2" },
         { name: "caskdependency", full_name: "homebrew/tap/caskdependency" },
       ].map { |formula| dependencies_arrays_hash.merge(formula) }
+      allow(Homebrew::Bundle::BrewDumper).to receive(:formulae).and_return(formulae_hash)
+
+      formulae_hash.each do |hash_formula|
+        name = hash_formula[:name]
+        full_name = hash_formula[:full_name]
+        tap_name = full_name.rpartition("/").first.presence || "homebrew/core"
+        tap = Tap.fetch(tap_name)
+        f = formula(name, tap:) { url "#{name}-1.0" }
+        stub_formula_loader f, full_name
+      end
+
       allow(Homebrew::Bundle::CaskDumper).to receive(:formula_dependencies).and_return(%w[caskdependency])
       expect(described_class.formulae_to_uninstall).to eql %w[
         c
@@ -93,6 +104,19 @@ RSpec.describe Homebrew::Bundle::Commands::Cleanup do
       expect(described_class.taps_to_untap).to eql(%w[z homebrew/tap])
     end
 
+    it "ignores formulae with .keepme references when computing which formulae to uninstall" do
+      name = full_name ="c"
+      allow(Homebrew::Bundle::BrewDumper).to receive(:formulae).and_return([{ name:, full_name: }])
+      f = formula(name) { url "#{name}-1.0" }
+      stub_formula_loader f, name
+
+      keg = instance_double(Keg)
+      allow(keg).to receive(:keepme_refs).and_return(["/some/file"])
+      allow(f).to receive(:installed_kegs).and_return([keg])
+
+      expect(described_class.formulae_to_uninstall).to be_empty
+    end
+
     it "computes which VSCode extensions to uninstall" do
       allow(Homebrew::Bundle::VscodeExtensionDumper).to receive(:extensions).and_return(%w[z])
       expect(described_class.vscode_extensions_to_uninstall).to eql(%w[z])