Add a tool warning when pod install does not work after adding a new test/watch/extension/other target with Xcode 16 (#156758)

Running `pod install` on Xcode projects with new test/targets in Xcode 16 will fail. Since this is a [Cocoapods bug](https://github.com/CocoaPods/CocoaPods/issues/12456), this PR adds a warning to the tool that links to a github work around and the current tracking issue.

Fixes https://github.com/flutter/flutter/issues/156733
<img width="567" alt="Screenshot 2024-10-14 at 14 48 39" src="https://github.com/user-attachments/assets/6befa601-4041-46fc-9ca2-f57662adda4a">

packages/flutter_tools/lib/src/macos/cocoapods.dart

@@ -502,6 +502,17 @@ class CocoaPods {
           );
         }
       }
+    } else if (stdout.contains('unknown ISA `PBXFileSystemSynchronizedRootGroup`')) {
+      // CocoaPods does not work with Xcode 16 since it has not yet been
+      // updated to handled synchronized
+      // groups/folders https://github.com/CocoaPods/CocoaPods/issues/12456
+      _logger.printError(
+        'Error: CocoaPods does not support Xcode 16 synchronized groups. '
+        'To fix your Xcode project, '
+        'see https://github.com/flutter/flutter/issues/156733#issuecomment-2415359014 '
+        'for a workaround.',
+        emphasis: true,
+      );
     }
   }
 

packages/flutter_tools/test/general.shard/macos/cocoapods_test.dart

@@ -517,6 +517,54 @@ Note: as of CocoaPods 1.0, `pod repo update` does not happen on `pod install` by
       );
     });
 
+    testUsingContext('throws if using a version of Cocoapods '
+        'that is unable to handle synchronized folders/groups', () async {
+      final FlutterProject projectUnderTest = setupProjectUnderTest();
+      pretendPodIsInstalled();
+      pretendPodVersionIs('100.0.0');
+      fileSystem.file(fileSystem.path.join('project', 'ios', 'Podfile'))
+        ..createSync()
+        ..writeAsStringSync('Existing Podfile');
+
+      fakeProcessManager.addCommand(
+        const FakeCommand(
+          command: <String>['pod', 'install', '--verbose'],
+          workingDirectory: 'project/ios',
+          environment: <String, String>{
+            'COCOAPODS_DISABLE_STATS': 'true',
+            'LANG': 'en_US.UTF-8',
+          },
+          exitCode: 1,
+          // This output is the output that a real CocoaPods install would generate.
+          stdout: '''
+### Command
+
+/opt/homebrew/Cellar/cocoapods/1.15.2_1/libexec/bin/pod install
+
+...
+### Error
+
+RuntimeError - `PBXGroup` attempted to initialize an object with unknown ISA `PBXFileSystemSynchronizedRootGroup` from attributes: `{"isa"=>"PBXFileSystemSynchronizedRootGroup", "explicitFileTypes"=>{}, "explicitFolders"=>[], "path"=>"RunnerTests", "sourceTree"=>"<group>"}`
+If this ISA was generated by Xcode please file an issue: https://github.com/CocoaPods/Xcodeproj/issues/new
+/opt/homebrew/Cellar/cocoapods/1.15.2_1/libexec/gems/xcodeproj-1.25.0/lib/xcodeproj/project/object.rb:359:in `rescue in object_with_uuid''',
+        ),
+      );
+
+      await expectLater(cocoaPodsUnderTest.processPods(
+        xcodeProject: projectUnderTest.ios,
+        buildMode: BuildMode.debug,
+      ), throwsToolExit());
+      expect(
+        logger.errorText,
+        contains(
+          'Error: CocoaPods does not support Xcode 16 synchronized groups. '
+          'To fix your Xcode project, '
+          'see https://github.com/flutter/flutter/issues/156733#issuecomment-2415359014 '
+          'for a workaround.',
+        ),
+      );
+    });
+
     testUsingContext('throws if plugin requires higher minimum iOS version using "platform"', () async {
       final FlutterProject projectUnderTest = setupProjectUnderTest();
       pretendPodIsInstalled();