Fix bundle update warnings about nil gemspecs

Sometimes, as a result of parallel installation of gems reading &
writing gemspecs concurrently during `bundle update`, some thread can
end up printing warnings like the following:

```
[/home/runner/work/rubygems/rubygems/bundler/tmp/2/gems/system/specifications/zeitwerk-2.4.2.gemspec] isn't a Gem::Specification (NilClass instead).
```

This commit fixes the issue by completely overriding rubygems installer
and removing all the unnecessary stuff. In particular, the
`Gem::Specification.reset` call that was constantly invalidating gem
specification caches and thus mutating shared state has been moved to
the main thread, after after installation of all gems is finished.

As a results, `bundle install` time is noticiably faster. A quick test
on my system (with ~500 gems installed) on an app with about ~100 locked
gems (to avoid resolution overhead) without extensions (to avoid
extension compilation overhead), with a fully loaded gem cache (to avoid
network overhead), it results in ~15% speed up in `bundle install` time:

```
$ hyperfine -p 'rm -rf vendor/bundle' 'bundle install' 'bundle _2.2.11_ install'
Benchmark #1: bundle install
  Time (mean ± σ):      5.713 s ±  0.387 s    [User: 5.215 s, System: 2.163 s]
  Range (min … max):    5.443 s …  6.610 s    10 runs

Benchmark #2: bundle _2.2.11_ install
  Time (mean ± σ):      6.549 s ±  0.106 s    [User: 6.087 s, System: 2.353 s]
  Range (min … max):    6.412 s …  6.773 s    10 runs

Summary
  'bundle install' ran
    1.15 ± 0.08 times faster than 'bundle _2.2.11_ install'
```

bundler/lib/bundler/installer.rb

@@ -89,6 +89,8 @@ def run(options)
         end
         install(options)
 
+        Gem::Specification.reset # invalidate gem specification cache so that installed gems are immediately available
+
         lock unless Bundler.frozen_bundle?
         Standalone.new(options[:standalone], @definition).generate if options[:standalone]
       end

bundler/lib/bundler/rubygems_gem_installer.rb

@@ -8,6 +8,53 @@ def check_executable_overwrite(filename)
       # Bundler needs to install gems regardless of binstub overwriting
     end
 
+    def install
+      pre_install_checks
+
+      run_pre_install_hooks
+
+      spec.loaded_from = spec_file
+
+      # Completely remove any previous gem files
+      FileUtils.rm_rf gem_dir
+      FileUtils.rm_rf spec.extension_dir
+
+      FileUtils.mkdir_p gem_dir, :mode => 0o755
+
+      extract_files
+
+      build_extensions
+      write_build_info_file
+      run_post_build_hooks
+
+      generate_bin
+      generate_plugins
+
+      write_spec
+      write_cache_file
+
+      say spec.post_install_message unless spec.post_install_message.nil?
+
+      run_post_install_hooks
+
+      spec
+    end
+
+    def generate_plugins
+      return unless Gem::Installer.instance_methods(false).include?(:generate_plugins)
+
+      latest = Gem::Specification.stubs_for(spec.name).first
+      return if latest && latest.version > spec.version
+
+      ensure_writable_dir @plugins_dir
+
+      if spec.plugins.empty?
+        remove_plugins_for(spec, @plugins_dir)
+      else
+        regenerate_plugins_for(spec, @plugins_dir)
+      end
+    end
+
     def pre_install_checks
       super && validate_bundler_checksum(options[:bundler_expected_checksum])
     end

bundler/spec/install/gemfile/sources_spec.rb

@@ -378,6 +378,123 @@
           end
         end
       end
+
+      context "when the lockfile has aggregated rubygems sources and newer versions of dependencies are available" do
+        before do
+          build_repo gem_repo2 do
+            build_gem "activesupport", "6.0.3.4" do |s|
+              s.add_dependency "concurrent-ruby", "~> 1.0", ">= 1.0.2"
+              s.add_dependency "i18n", ">= 0.7", "< 2"
+              s.add_dependency "minitest", "~> 5.1"
+              s.add_dependency "tzinfo", "~> 1.1"
+              s.add_dependency "zeitwerk", "~> 2.2", ">= 2.2.2"
+            end
+
+            build_gem "activesupport", "6.1.2.1" do |s|
+              s.add_dependency "concurrent-ruby", "~> 1.0", ">= 1.0.2"
+              s.add_dependency "i18n", ">= 1.6", "< 2"
+              s.add_dependency "minitest", ">= 5.1"
+              s.add_dependency "tzinfo", "~> 2.0"
+              s.add_dependency "zeitwerk", "~> 2.3"
+            end
+
+            build_gem "concurrent-ruby", "1.1.8"
+            build_gem "concurrent-ruby", "1.1.9"
+            build_gem "connection_pool", "2.2.3"
+
+            build_gem "i18n", "1.8.9" do |s|
+              s.add_dependency "concurrent-ruby", "~> 1.0"
+            end
+
+            build_gem "minitest", "5.14.3"
+            build_gem "rack", "2.2.3"
+            build_gem "redis", "4.2.5"
+
+            build_gem "sidekiq", "6.1.3" do |s|
+              s.add_dependency "connection_pool", ">= 2.2.2"
+              s.add_dependency "rack", "~> 2.0"
+              s.add_dependency "redis", ">= 4.2.0"
+            end
+
+            build_gem "thread_safe", "0.3.6"
+
+            build_gem "tzinfo", "1.2.9" do |s|
+              s.add_dependency "thread_safe", "~> 0.1"
+            end
+
+            build_gem "tzinfo", "2.0.4" do |s|
+              s.add_dependency "concurrent-ruby", "~> 1.0"
+            end
+
+            build_gem "zeitwerk", "2.4.2"
+          end
+
+          build_repo gem_repo3 do
+            build_gem "sidekiq-pro", "5.2.1" do |s|
+              s.add_dependency "connection_pool", ">= 2.2.3"
+              s.add_dependency "sidekiq", ">= 6.1.0"
+            end
+          end
+
+          gemfile <<-G
+            # frozen_string_literal: true
+
+            source "#{file_uri_for(gem_repo2)}"
+
+            gem "activesupport"
+
+            source "#{file_uri_for(gem_repo3)}" do
+              gem "sidekiq-pro"
+            end
+          G
+
+          lockfile <<~L
+            GEM
+              remote: #{file_uri_for(gem_repo2)}/
+              remote: #{file_uri_for(gem_repo3)}/
+              specs:
+                activesupport (6.0.3.4)
+                  concurrent-ruby (~> 1.0, >= 1.0.2)
+                  i18n (>= 0.7, < 2)
+                  minitest (~> 5.1)
+                  tzinfo (~> 1.1)
+                  zeitwerk (~> 2.2, >= 2.2.2)
+                concurrent-ruby (1.1.8)
+                connection_pool (2.2.3)
+                i18n (1.8.9)
+                  concurrent-ruby (~> 1.0)
+                minitest (5.14.3)
+                rack (2.2.3)
+                redis (4.2.5)
+                sidekiq (6.1.3)
+                  connection_pool (>= 2.2.2)
+                  rack (~> 2.0)
+                  redis (>= 4.2.0)
+                sidekiq-pro (5.2.1)
+                  connection_pool (>= 2.2.3)
+                  sidekiq (>= 6.1.0)
+                thread_safe (0.3.6)
+                tzinfo (1.2.9)
+                  thread_safe (~> 0.1)
+                zeitwerk (2.4.2)
+
+            PLATFORMS
+              #{specific_local_platform}
+
+            DEPENDENCIES
+              activesupport
+              sidekiq-pro!
+
+            BUNDLED WITH
+               #{Bundler::VERSION}
+          L
+        end
+
+        it "upgrades gems when running bundle update, without printing any warnings or errors" do
+          bundle "update --all"
+          expect(err).to be_empty
+        end
+      end
     end
 
     context "with a gem that is only found in the wrong source" do