Fix bundle binstub broken by gem update --system on Homebrew ruby

lib/rubygems/commands/setup_command.rb

@@ -355,36 +355,51 @@ def install_default_bundler_gem(bin_dir)
       loaded_from = current_default_spec.loaded_from
       File.delete(loaded_from)
 
-      # Remove previous default gem executables if they were not shadowed by a regular gem
-      FileUtils.rm_rf current_default_spec.full_gem_path if all_specs_current_version.size == 1
+      previous_specs_dir = File.dirname(loaded_from)
+
+      # Remove previous default gem executables if they were not shadowed by a
+      # regular gem. They live under the same root as the previous default
+      # gemspec, which is not necessarily default_dir.
+      if all_specs_current_version.size == 1
+        previous_root = File.dirname(File.dirname(previous_specs_dir))
+        FileUtils.rm_rf File.join(previous_root, "gems", current_default_spec.full_name)
+      end
 
-      File.dirname(loaded_from)
+      previous_specs_dir
     else
       target_specs_dir = File.join(default_dir, "specifications", "default")
       mkdir_p target_specs_dir, mode: 0o755
       target_specs_dir
     end
 
+    # Root directory that specs_dir belongs to. It may differ from default_dir
+    # when Gem.default_specifications_dir is customized to live under a
+    # different root, like Homebrew does. Executables must be extracted under
+    # the same root as the default gemspec, since that's where activation of
+    # the default gem will look for them.
+    bundler_install_dir = File.dirname(File.dirname(specs_dir))
+
     new_bundler_spec = Gem::Specification.load("bundler.gemspec")
     full_name = new_bundler_spec.full_name
     gemspec_path = "#{full_name}.gemspec"
 
     default_spec_path = File.join(specs_dir, gemspec_path)
     Gem.write_binary(default_spec_path, new_bundler_spec.to_ruby)
 
-    bundler_spec = Gem::Specification.load(default_spec_path)
-
     # Remove gemspec that was same version of vendored bundler.
     normal_gemspec = File.join(default_dir, "specifications", gemspec_path)
     if File.file? normal_gemspec
       File.delete normal_gemspec
     end
 
-    # Remove gem files that were same version of vendored bundler.
-    if File.directory? bundler_spec.gems_dir
-      Dir.entries(bundler_spec.gems_dir).
-        select {|default_gem| File.basename(default_gem) == full_name }.
-        each {|default_gem| rm_r File.join(bundler_spec.gems_dir, default_gem) }
+    # Remove gem files that were same version of vendored bundler. A regular
+    # gem lives under default_dir, which is not necessarily the same root as
+    # the default gemspec.
+    normal_gems_dir = File.join(default_dir, "gems")
+    if File.directory? normal_gems_dir
+      Dir.entries(normal_gems_dir).
+        select {|normal_gem| File.basename(normal_gem) == full_name }.
+        each {|normal_gem| rm_r File.join(normal_gems_dir, normal_gem) }
     end
 
     require_relative "../installer"
@@ -397,14 +412,14 @@ def install_default_bundler_gem(bin_dir)
         format_executable: options[:format_executable],
         force: options[:force],
         bin_dir: bin_dir,
-        install_dir: default_dir,
+        install_dir: bundler_install_dir,
         wrappers: true
       )
-      # We need to install only executable and default spec files.
-      # lib/bundler.rb and lib/bundler/* are available under the site_ruby directory.
+      # We only need to install the executables here. The default spec was
+      # already written above, and lib/bundler.rb and lib/bundler/* are
+      # available under the site_ruby directory.
       installer.extract_bin
       installer.generate_bin
-      installer.write_default_spec
     ensure
       FileUtils.rm_f built_gem
     end

test/rubygems/test_gem_commands_setup_command.rb

@@ -241,17 +241,44 @@ def test_install_default_bundler_gem
   def test_install_default_bundler_gem_with_default_gems_not_installed_at_default_dir
     @cmd.extend FileUtils
 
+    # Simulate Homebrew's layout, where Gem.default_dir is moved to a
+    # different root, while Gem.default_specifications_dir stays inside the
+    # ruby install tree.
     gemhome2 = File.join(@tempdir, "gemhome2")
     Gem.instance_variable_set(:@default_dir, gemhome2)
 
     FileUtils.mkdir_p gemhome2
     bin_dir = File.join(gemhome2, "bin")
 
+    previous_default_gem_dir = File.join(@gemhome, "gems", "bundler-1.15.4")
+    write_file File.join(previous_default_gem_dir, "exe", "bundle")
+
+    # A regular gem of the same version installed at the default dir, which is
+    # promoted to the default gem and must be removed. Its files live under
+    # default_dir, not under the default gemspec root.
+    normal_gem_dir = File.join(gemhome2, "gems", "bundler-#{bundler_version}")
+    write_file File.join(normal_gem_dir, "lib", "bundler.rb")
+
     @cmd.install_default_bundler_gem bin_dir
 
     # expect to remove other versions of bundler gemspecs on default specification directory.
     assert_path_not_exist previous_bundler_specification_path
     assert_path_exist new_bundler_specification_path
+
+    # expect to remove the previous default version executables, which live
+    # next to the removed gemspec, not under the new default dir.
+    assert_path_not_exist previous_default_gem_dir
+
+    # expect to remove the promoted regular gem's files under default_dir.
+    assert_path_not_exist normal_gem_dir
+
+    # expect executables to be installed under the same root as the default
+    # gemspec, since that's where activation of the default gem looks for them.
+    spec = Gem::Specification.load(new_bundler_specification_path)
+    spec.executables.each do |e|
+      assert_path_exist File.join(@gemhome, "gems", spec.full_name, spec.bindir, e)
+    end
+    assert_path_not_exist File.join(gemhome2, "gems", spec.full_name)
   end
 
   def test_install_default_bundler_gem_with_force_flag