Fix synced folder issues: configFiles duplicate, group insertion, and directory-level membershipExceptions

[AlexNsbmr]

Description

Three related fixes for defaultSourceDirectoryType: syncedFolder support.

1. configFiles creating duplicate groups

When using configFiles that reference paths inside a synced folder source, a duplicate PBXGroup is created alongside the PBXFileSystemSynchronizedRootGroup.

options:
  defaultSourceDirectoryType: syncedFolder

configFiles:
  Debug: Sources/Config/debug.xcconfig
  Release: Sources/Config/release.xcconfig

targets:
  App:
    sources: [Sources]

Root cause: getContainedFileReference() always creates a PBXGroup hierarchy via getGroup(), regardless of whether the file lives inside a synced folder. Same class of issue as #1602, but for configFiles.

Fix: Return a file reference with sourceTree: .sourceRoot when the path is inside a synced folder, skipping group creation entirely.

2. Root group duplication for paths inside synced folders

When multiple targets reference a synced folder path (e.g., extension targets with type: syncedFolder), getGroup() inserts the group into rootGroups, causing a duplicate entry in the project navigator.

Fix: Skip rootGroups insertion when the path is inside an existing synced folder.

3. Directory-level membershipExceptions not working

When using includes on a synced folder source, findExceptions adds directory names to membershipExceptions instead of individual file paths. Xcode does not recursively exclude directory contents from membership exceptions, leading to:

• "Multiple commands produce Info.plist" build errors (e.g., Supporting Files/ directory in exceptions doesn't exclude Supporting Files/Info.plist)
• Wrong target membership for files in non-included directories (e.g., files incorrectly added to extension targets)

# Example: extension target cherry-picking files from shared synced folder
NotificationServiceExtension:
  sources:
    - path: Sources
      type: syncedFolder
      includes:
        - Notifications/NotificationPayload.swift

Fix: Recurse into non-included directories in findExceptions to list individual file paths instead of directory names.

Tests

• Existing test: does not create duplicate group for configFiles inside synced folder
• Existing tests for synced folder includes cover the membershipExceptions behavior

Environment

• XcodeGen: 2.45.3
• Xcode: 16
• macOS: Sequoia