diff --git a/spec/bundler/commands/newgem_spec.rb b/spec/bundler/commands/newgem_spec.rb
index 199340b1314ccd..53d0f9d6eb6f53 100644
--- a/spec/bundler/commands/newgem_spec.rb
+++ b/spec/bundler/commands/newgem_spec.rb
@@ -36,22 +36,25 @@ def bundle_exec_standardrb
     sys_exec("git config --global user.name 'Bundler User'")
     sys_exec("git config --global user.email user@example.com")
     sys_exec("git config --global github.user bundleuser")
+
+    global_config "BUNDLE_GEM__MIT" => "false", "BUNDLE_GEM__TEST" => "false", "BUNDLE_GEM__COC" => "false", "BUNDLE_GEM__LINTER" => "false",
+                  "BUNDLE_GEM__CI" => "false", "BUNDLE_GEM__CHANGELOG" => "false"
   end
 
   describe "git repo initialization" do
-    it "generates a gem skeleton with a .git folder", :readline do
+    it "generates a gem skeleton with a .git folder" do
       bundle "gem #{gem_name}"
       gem_skeleton_assertions
       expect(bundled_app("#{gem_name}/.git")).to exist
     end
 
-    it "generates a gem skeleton with a .git folder when passing --git", :readline do
+    it "generates a gem skeleton with a .git folder when passing --git" do
       bundle "gem #{gem_name} --git"
       gem_skeleton_assertions
       expect(bundled_app("#{gem_name}/.git")).to exist
     end
 
-    it "generates a gem skeleton without a .git folder when passing --no-git", :readline do
+    it "generates a gem skeleton without a .git folder when passing --no-git" do
       bundle "gem #{gem_name} --no-git"
       gem_skeleton_assertions
       expect(bundled_app("#{gem_name}/.git")).not_to exist
@@ -62,7 +65,9 @@ def bundle_exec_standardrb
         Dir.mkdir(bundled_app("path with spaces"))
       end
 
-      it "properly initializes git repo", :readline do
+      it "properly initializes git repo" do
+        skip "path with spaces needs special handling on Windows" if Gem.win_platform?
+
         bundle "gem #{gem_name}", dir: bundled_app("path with spaces")
         expect(bundled_app("path with spaces/#{gem_name}/.git")).to exist
       end
@@ -131,7 +136,7 @@ def bundle_exec_standardrb
     before do
       bundle "gem #{gem_name} --changelog"
     end
-    it "generates a gem skeleton with a CHANGELOG", :readline do
+    it "generates a gem skeleton with a CHANGELOG" do
       gem_skeleton_assertions
       expect(bundled_app("#{gem_name}/CHANGELOG.md")).to exist
     end
@@ -141,7 +146,7 @@ def bundle_exec_standardrb
     before do
       bundle "gem #{gem_name} --no-changelog"
     end
-    it "generates a gem skeleton without a CHANGELOG", :readline do
+    it "generates a gem skeleton without a CHANGELOG" do
       gem_skeleton_assertions
       expect(bundled_app("#{gem_name}/CHANGELOG.md")).to_not exist
     end
@@ -150,6 +155,7 @@ def bundle_exec_standardrb
   shared_examples_for "--rubocop flag" do
     context "is deprecated", bundler: "< 3" do
       before do
+        global_config "BUNDLE_GEM__LINTER" => nil
         bundle "gem #{gem_name} --rubocop"
       end
 
@@ -303,49 +309,49 @@ def bundle_exec_standardrb
     end
   end
 
-  it "has no rubocop offenses when using --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     bundle "gem #{gem_name} --linter=rubocop"
     bundle_exec_rubocop
     expect(last_command).to be_success
   end
 
-  it "has no rubocop offenses when using --ext=c and --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --ext=c and --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     bundle "gem #{gem_name} --ext=c --linter=rubocop"
     bundle_exec_rubocop
     expect(last_command).to be_success
   end
 
-  it "has no rubocop offenses when using --ext=c, --test=minitest, and --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --ext=c, --test=minitest, and --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     bundle "gem #{gem_name} --ext=c --test=minitest --linter=rubocop"
     bundle_exec_rubocop
     expect(last_command).to be_success
   end
 
-  it "has no rubocop offenses when using --ext=c, --test=rspec, and --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --ext=c, --test=rspec, and --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     bundle "gem #{gem_name} --ext=c --test=rspec --linter=rubocop"
     bundle_exec_rubocop
     expect(last_command).to be_success
   end
 
-  it "has no rubocop offenses when using --ext=c, --test=test-unit, and --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --ext=c, --test=test-unit, and --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     bundle "gem #{gem_name} --ext=c --test=test-unit --linter=rubocop"
     bundle_exec_rubocop
     expect(last_command).to be_success
   end
 
-  it "has no standard offenses when using --linter=standard flag", :readline do
+  it "has no standard offenses when using --linter=standard flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     bundle "gem #{gem_name} --linter=standard"
     bundle_exec_standardrb
     expect(last_command).to be_success
   end
 
-  it "has no rubocop offenses when using --ext=rust and --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --ext=rust and --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     skip "RubyGems incompatible with Rust builder" if ::Gem::Version.new("3.3.11") > ::Gem.rubygems_version
 
@@ -354,7 +360,7 @@ def bundle_exec_standardrb
     expect(last_command).to be_success
   end
 
-  it "has no rubocop offenses when using --ext=rust, --test=minitest, and --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --ext=rust, --test=minitest, and --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     skip "RubyGems incompatible with Rust builder" if ::Gem::Version.new("3.3.11") > ::Gem.rubygems_version
 
@@ -363,7 +369,7 @@ def bundle_exec_standardrb
     expect(last_command).to be_success
   end
 
-  it "has no rubocop offenses when using --ext=rust, --test=rspec, and --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --ext=rust, --test=rspec, and --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     skip "RubyGems incompatible with Rust builder" if ::Gem::Version.new("3.3.11") > ::Gem.rubygems_version
 
@@ -372,7 +378,7 @@ def bundle_exec_standardrb
     expect(last_command).to be_success
   end
 
-  it "has no rubocop offenses when using --ext=rust, --test=test-unit, and --linter=rubocop flag", :readline do
+  it "has no rubocop offenses when using --ext=rust, --test=test-unit, and --linter=rubocop flag" do
     skip "ruby_core has an 'ast.rb' file that gets in the middle and breaks this spec" if ruby_core?
     skip "RubyGems incompatible with Rust builder" if ::Gem::Version.new("3.3.11") > ::Gem.rubygems_version
 
@@ -399,7 +405,7 @@ def bundle_exec_standardrb
     end
   end
 
-  context "README.md", :readline do
+  context "README.md" do
     context "git config github.user present" do
       before do
         bundle "gem #{gem_name}"
@@ -424,12 +430,12 @@ def bundle_exec_standardrb
     end
   end
 
-  it "creates a new git repository", :readline do
+  it "creates a new git repository" do
     bundle "gem #{gem_name}"
     expect(bundled_app("#{gem_name}/.git")).to exist
   end
 
-  context "when git is not available", :readline do
+  context "when git is not available" do
     # This spec cannot have `git` available in the test env
     before do
       load_paths = [lib_dir, spec_dir]
@@ -451,7 +457,7 @@ def bundle_exec_standardrb
     end
   end
 
-  it "generates a valid gemspec", :readline, :ruby_repo do
+  it "generates a valid gemspec", :ruby_repo do
     bundle "gem newgem --bin"
 
     prepare_gemspec(bundled_app("newgem", "newgem.gemspec"))
@@ -464,7 +470,7 @@ def bundle_exec_standardrb
     expect(last_command.stdboth).not_to include("ERROR")
   end
 
-  context "gem naming with relative paths", :readline do
+  context "gem naming with relative paths" do
     it "resolves ." do
       create_temporary_dir("tmp")
 
@@ -557,8 +563,12 @@ def create_temporary_dir(dir)
 
       expect(bundled_app("#{gem_name}/bin/setup")).to exist
       expect(bundled_app("#{gem_name}/bin/console")).to exist
-      expect(bundled_app("#{gem_name}/bin/setup")).to be_executable
-      expect(bundled_app("#{gem_name}/bin/console")).to be_executable
+
+      unless Gem.win_platform?
+        expect(bundled_app("#{gem_name}/bin/setup")).to be_executable
+        expect(bundled_app("#{gem_name}/bin/console")).to be_executable
+      end
+
       expect(bundled_app("#{gem_name}/bin/setup").read).to start_with("#!")
       expect(bundled_app("#{gem_name}/bin/console").read).to start_with("#!")
     end
@@ -870,7 +880,7 @@ def create_temporary_dir(dir)
       end
     end
 
-    context "gem.test set to rspec and --test with no arguments", :hint_text do
+    context "gem.test set to rspec and --test with no arguments" do
       before do
         bundle "config set gem.test rspec"
         bundle "gem #{gem_name} --test"
@@ -887,10 +897,12 @@ def create_temporary_dir(dir)
       end
     end
 
-    context "gem.test setting set to false and --test with no arguments", :hint_text do
+    context "gem.test setting set to false and --test with no arguments", :readline do
       before do
         bundle "config set gem.test false"
-        bundle "gem #{gem_name} --test"
+        bundle "gem #{gem_name} --test" do |input, _, _|
+          input.puts
+        end
       end
 
       it "asks to generate test files" do
@@ -904,9 +916,12 @@ def create_temporary_dir(dir)
       it_behaves_like "test framework is absent"
     end
 
-    context "gem.test setting not set and --test with no arguments", :hint_text do
+    context "gem.test setting not set and --test with no arguments", :readline do
       before do
-        bundle "gem #{gem_name} --test"
+        global_config "BUNDLE_GEM__TEST" => nil
+        bundle "gem #{gem_name} --test" do |input, _, _|
+          input.puts
+        end
       end
 
       it "asks to generate test files" do
@@ -1009,7 +1024,7 @@ def create_temporary_dir(dir)
       end
     end
 
-    context "gem.ci set to github and --ci with no arguments", :hint_text do
+    context "gem.ci set to github and --ci with no arguments" do
       before do
         bundle "config set gem.ci github"
         bundle "gem #{gem_name} --ci"
@@ -1024,10 +1039,12 @@ def create_temporary_dir(dir)
       end
     end
 
-    context "gem.ci setting set to false and --ci with no arguments", :hint_text do
+    context "gem.ci setting set to false and --ci with no arguments", :readline do
       before do
         bundle "config set gem.ci false"
-        bundle "gem #{gem_name} --ci"
+        bundle "gem #{gem_name} --ci" do |input, _, _|
+          input.puts "github"
+        end
       end
 
       it "asks to setup CI" do
@@ -1039,9 +1056,12 @@ def create_temporary_dir(dir)
       end
     end
 
-    context "gem.ci setting not set and --ci with no arguments", :hint_text do
+    context "gem.ci setting not set and --ci with no arguments", :readline do
       before do
-        bundle "gem #{gem_name} --ci"
+        global_config "BUNDLE_GEM__CI" => nil
+        bundle "gem #{gem_name} --ci" do |input, _, _|
+          input.puts "github"
+        end
       end
 
       it "asks to setup CI" do
@@ -1111,6 +1131,7 @@ def create_temporary_dir(dir)
 
     context "gem.rubocop setting set to true", bundler: "< 3" do
       before do
+        global_config "BUNDLE_GEM__LINTER" => nil
         bundle "config set gem.rubocop true"
         bundle "gem #{gem_name}"
       end
@@ -1130,7 +1151,7 @@ def create_temporary_dir(dir)
       end
     end
 
-    context "gem.linter set to rubocop and --linter with no arguments", :hint_text do
+    context "gem.linter set to rubocop and --linter with no arguments" do
       before do
         bundle "config set gem.linter rubocop"
         bundle "gem #{gem_name} --linter"
@@ -1145,10 +1166,12 @@ def create_temporary_dir(dir)
       end
     end
 
-    context "gem.linter setting set to false and --linter with no arguments", :hint_text do
+    context "gem.linter setting set to false and --linter with no arguments", :readline do
       before do
         bundle "config set gem.linter false"
-        bundle "gem #{gem_name} --linter"
+        bundle "gem #{gem_name} --linter" do |input, _, _|
+          input.puts "rubocop"
+        end
       end
 
       it "asks to setup a linter" do
@@ -1160,9 +1183,12 @@ def create_temporary_dir(dir)
       end
     end
 
-    context "gem.linter setting not set and --linter with no arguments", :hint_text do
+    context "gem.linter setting not set and --linter with no arguments", :readline do
       before do
-        bundle "gem #{gem_name} --linter"
+        global_config "BUNDLE_GEM__LINTER" => nil
+        bundle "gem #{gem_name} --linter" do |input, _, _|
+          input.puts "rubocop"
+        end
       end
 
       it "asks to setup a linter" do
@@ -1185,7 +1211,7 @@ def create_temporary_dir(dir)
     end
   end
 
-  context "testing --mit and --coc options against bundle config settings", :readline do
+  context "testing --mit and --coc options against bundle config settings" do
     let(:gem_name) { "test-gem" }
 
     let(:require_path) { "test/gem" }
@@ -1288,7 +1314,7 @@ def create_temporary_dir(dir)
     end
   end
 
-  context "testing --github-username option against git and bundle config settings", :readline do
+  context "testing --github-username option against git and bundle config settings" do
     context "without git config set" do
       before do
         sys_exec("git config --global --unset github.user")
@@ -1325,7 +1351,7 @@ def create_temporary_dir(dir)
     end
   end
 
-  context "testing github_username bundle config against git config settings", :readline do
+  context "testing github_username bundle config against git config settings" do
     context "without git config set" do
       before do
         sys_exec("git config --global --unset github.user")
@@ -1339,7 +1365,7 @@ def create_temporary_dir(dir)
     end
   end
 
-  context "gem naming with underscore", :readline do
+  context "gem naming with underscore" do
     let(:gem_name) { "test_gem" }
 
     let(:require_path) { "test_gem" }
@@ -1485,7 +1511,7 @@ def create_temporary_dir(dir)
     end
   end
 
-  context "gem naming with dashed", :readline do
+  context "gem naming with dashed" do
     let(:gem_name) { "test-gem" }
 
     let(:require_path) { "test/gem" }
@@ -1506,7 +1532,7 @@ def create_temporary_dir(dir)
   end
 
   describe "uncommon gem names" do
-    it "can deal with two dashes", :readline do
+    it "can deal with two dashes" do
       bundle "gem a--a"
 
       expect(bundled_app("a--a/a--a.gemspec")).to exist
@@ -1536,7 +1562,7 @@ def create_temporary_dir(dir)
     end
   end
 
-  describe "#ensure_safe_gem_name", :readline do
+  describe "#ensure_safe_gem_name" do
     before do
       bundle "gem #{subject}", raise_on_error: false
     end
@@ -1564,7 +1590,7 @@ def create_temporary_dir(dir)
 
   context "on first run", :readline do
     it "asks about test framework" do
-      global_config "BUNDLE_GEM__MIT" => "false", "BUNDLE_GEM__COC" => "false"
+      global_config "BUNDLE_GEM__TEST" => nil
 
       bundle "gem foobar" do |input, _, _|
         input.puts "rspec"
@@ -1587,7 +1613,7 @@ def create_temporary_dir(dir)
     end
 
     it "asks about CI service" do
-      global_config "BUNDLE_GEM__TEST" => "false", "BUNDLE_GEM__MIT" => "false", "BUNDLE_GEM__COC" => "false", "BUNDLE_GEM__LINTER" => "false"
+      global_config "BUNDLE_GEM__CI" => nil
 
       bundle "gem foobar" do |input, _, _|
         input.puts "github"
@@ -1597,7 +1623,7 @@ def create_temporary_dir(dir)
     end
 
     it "asks about MIT license" do
-      global_config "BUNDLE_GEM__TEST" => "false", "BUNDLE_GEM__COC" => "false", "BUNDLE_GEM__CI" => "false", "BUNDLE_GEM__LINTER" => "false"
+      global_config "BUNDLE_GEM__MIT" => nil
 
       bundle "config list"
 
@@ -1609,7 +1635,7 @@ def create_temporary_dir(dir)
     end
 
     it "asks about CoC" do
-      global_config "BUNDLE_GEM__MIT" => "false", "BUNDLE_GEM__TEST" => "false", "BUNDLE_GEM__CI" => "false", "BUNDLE_GEM__LINTER" => "false"
+      global_config "BUNDLE_GEM__COC" => nil
 
       bundle "gem foobar" do |input, _, _|
         input.puts "yes"
@@ -1619,8 +1645,7 @@ def create_temporary_dir(dir)
     end
 
     it "asks about CHANGELOG" do
-      global_config "BUNDLE_GEM__MIT" => "false", "BUNDLE_GEM__TEST" => "false", "BUNDLE_GEM__CI" => "false", "BUNDLE_GEM__LINTER" => "false",
-                    "BUNDLE_GEM__COC" => "false"
+      global_config "BUNDLE_GEM__CHANGELOG" => nil
 
       bundle "gem foobar" do |input, _, _|
         input.puts "yes"
@@ -1630,7 +1655,7 @@ def create_temporary_dir(dir)
     end
   end
 
-  context "on conflicts with a previously created file", :readline do
+  context "on conflicts with a previously created file" do
     it "should fail gracefully" do
       FileUtils.touch(bundled_app("conflict-foobar"))
       bundle "gem conflict-foobar", raise_on_error: false
@@ -1639,7 +1664,7 @@ def create_temporary_dir(dir)
     end
   end
 
-  context "on conflicts with a previously created directory", :readline do
+  context "on conflicts with a previously created directory" do
     it "should succeed" do
       FileUtils.mkdir_p(bundled_app("conflict-foobar/Gemfile"))
       bundle "gem conflict-foobar"
diff --git a/spec/bundler/other/major_deprecation_spec.rb b/spec/bundler/other/major_deprecation_spec.rb
index 939b68a0bbf6c9..e7577d38b49074 100644
--- a/spec/bundler/other/major_deprecation_spec.rb
+++ b/spec/bundler/other/major_deprecation_spec.rb
@@ -618,7 +618,12 @@
     pending "fails with a helpful message", bundler: "3"
   end
 
-  describe "deprecating rubocop", :readline do
+  describe "deprecating rubocop" do
+    before do
+      global_config "BUNDLE_GEM__MIT" => "false", "BUNDLE_GEM__TEST" => "false", "BUNDLE_GEM__COC" => "false",
+                    "BUNDLE_GEM__CI" => "false", "BUNDLE_GEM__CHANGELOG" => "false"
+    end
+
     context "bundle gem --rubocop" do
       before do
         bundle "gem my_new_gem --rubocop", raise_on_error: false
diff --git a/spec/bundler/support/helpers.rb b/spec/bundler/support/helpers.rb
index 1ad9cc78ca19cc..dbb8b8152b5d2d 100644
--- a/spec/bundler/support/helpers.rb
+++ b/spec/bundler/support/helpers.rb
@@ -226,12 +226,20 @@ def all_commands_output
     end
 
     def config(config = nil, path = bundled_app(".bundle/config"))
-      return Psych.load_file(path) unless config
+      current = File.exist?(path) ? Psych.load_file(path) : {}
+      return current unless config
+
+      current = {} if current.empty?
+
       FileUtils.mkdir_p(File.dirname(path))
-      File.open(path, "w") do |f|
-        f.puts config.to_yaml
+
+      new_config = current.merge(config).compact
+
+      File.open(path, "w+") do |f|
+        f.puts new_config.to_yaml
       end
-      config
+
+      new_config
     end
 
     def global_config(config = nil)