Improve default gem handling

If a gem is specified in the Gemfile (or resolved as a transitive
dependency), it's always resolved from remote/installed sources. Default
gems are only used as a fallback for gems not included in the bundle.

I believe this leads to more consistent behavior and more portable apps,
since all gems will be installed to the configured bundle path,
regardless of whether they are default gems or not.

bundler/lib/bundler/rubygems_integration.rb

@@ -509,7 +509,7 @@ def path_separator
     end
 
     def all_specs
-      Gem::Specification.stubs.map do |stub|
+      Gem::Specification.stubs.reject(&:default_gem?).map do |stub|
         StubSpecification.from_stub(stub)
       end
     end

bundler/lib/bundler/source/rubygems.rb

@@ -225,11 +225,7 @@ def cached_built_in_gem(spec)
         cached_path = cached_path(spec)
         if cached_path.nil?
           remote_spec = remote_specs.search(spec).first
-          if remote_spec
-            cached_path = fetch_gem(remote_spec)
-          else
-            Bundler.ui.warn "#{spec.full_name} is built in to Ruby, and can't be cached because your Gemfile doesn't have any sources that contain it."
-          end
+          cached_path = fetch_gem(remote_spec)
         end
         cached_path
       end

bundler/spec/cache/gems_spec.rb

@@ -102,8 +102,8 @@
 
     it "uses builtin gems when installing to system gems" do
       bundle "config set path.system true"
-      install_gemfile %(source "#{file_uri_for(gem_repo1)}"; gem 'json', '#{default_json_version}'), verbose: true
-      expect(out).to include("Using json #{default_json_version}")
+      install_gemfile %(source "#{file_uri_for(gem_repo2)}"; gem 'json', '#{default_json_version}'), verbose: true
+      expect(out).to include("Installing json #{default_json_version}")
     end
 
     it "caches remote and builtin gems" do
@@ -143,19 +143,6 @@
       bundle "install --local"
       expect(the_bundle).to include_gems("builtin_gem_2 1.0.2")
     end
-
-    it "errors if the builtin gem isn't available to cache" do
-      bundle "config set path.system true"
-
-      install_gemfile <<-G
-        source "#{file_uri_for(gem_repo1)}"
-        gem 'json', '#{default_json_version}'
-      G
-
-      bundle :cache, raise_on_error: false
-      expect(exitstatus).to_not eq(0)
-      expect(err).to include("json-#{default_json_version} is built in to Ruby, and can't be cached")
-    end
   end
 
   describe "when there are also git sources" do

bundler/spec/commands/open_spec.rb

@@ -164,7 +164,6 @@
 
       install_gemfile <<-G
         source "#{file_uri_for(gem_repo1)}"
-        gem "json"
       G
     end
 

bundler/spec/runtime/setup_spec.rb

@@ -1281,6 +1281,10 @@ def lock_with(ruby_version = nil)
 
   describe "with gemified standard libraries" do
     it "does not load Digest", :ruby_repo do
+      build_repo2 do
+        build_gem "digest"
+      end
+
       build_git "bar", gemspec: false do |s|
         s.write "lib/bar/version.rb", %(BAR_VERSION = '1.0')
         s.write "bar.gemspec", <<-G
@@ -1299,7 +1303,7 @@ def lock_with(ruby_version = nil)
       end
 
       gemfile <<-G
-        source "#{file_uri_for(gem_repo1)}"
+        source "#{file_uri_for(gem_repo2)}"
         gem "bar", :git => "#{lib_path("bar-1.0")}"
       G