CocoaPods does not work with Xcode 16 since it has not yet been updated to handled synchronized groups/folders CocoaPods/CocoaPods#12456

Add flutter tooling support that detects the Xcode project contains PBXFileSystemSynchronizedRootGroup, and outputs a warning linking to this issue or https://stackoverflow.com/a/79003357/431116 or similar with the workaround.

Around here check if the error contains "unknown ISA `PBXFileSystemSynchronizedRootGroup`"

From https://discord.com/channels/608014603317936148/1295165633931120642/1295166301626564628

The issue encountered after adding the native Unit/UI tests target for macOS in the example app by following Flutter instructions of Enabling XCTests or XCUITests, which prevent running or building the example app, causing failure when running pod install or flutter run -d macos

• Use latest version of Flutter stable channel (Dart 3.5.3, Flutter 3.24.3) with latest CocoaPods (1.15.2) and Xcode 16.
• Clone flutter/packages repo and cd into a plugin that have support for macOS but doesn't have native UI/Unit tests. https://github.com/flutter/packages/tree/main/packages/image_picker/image_picker_macos/example/macos is an example.
• Run pod install in the example macOS app or run the Flutter app directly with flutter run -d macos.
• Follow the steps in https://github.com/flutter/flutter/blob/master/docs/ecosystem/testing/Plugin-Tests.md#enabling-xctests-or-xcuitests to enable XCTests or XCUITests.
• Run the Unit test directly in Xcode, works as expected.

### 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'

Originally posted by @jmagman in #153402 (comment)