Fix synced folder issues: configFiles duplicate, group insertion, and directory-level membershipExceptions (#1607)

* Fix configFiles creating duplicate group inside synced folder

When configFiles reference paths inside a synced folder source,
getContainedFileReference() created a separate PBXGroup hierarchy
that duplicated the PBXFileSystemSynchronizedRootGroup already
managing those files.

Skip group creation in getContainedFileReference when the file
path falls inside an existing synced folder root.

Fixes the same class of issue as #1602, but for configFiles
rather than target sources.

* Fix synced folder group duplication and directory-level membershipExceptions

- Prevent rootGroups insertion for paths inside synced folders,
  avoiding duplicate PBXGroup alongside PBXFileSystemSynchronizedRootGroup
- Recurse into non-included directories in findExceptions to list
  individual file paths instead of directory names, since Xcode does
  not recursively exclude directory contents from membershipExceptions

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Update test: expect individual file paths instead of directory names in exceptions

Xcode does not recursively exclude directory contents from
membershipExceptions, so the correct behavior is to list individual
files rather than directory names.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Use basePath instead of project.basePath for synced folder checks

When XcodeGen is run with --project-directory, the computed basePath
property accounts for the different output location. Using project.basePath
would resolve paths incorrectly in that scenario.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: AlexNsbmr

Sources/XcodeGenKit/SourceGenerator.swift

@@ -206,7 +206,13 @@ class SourceGenerator {
         let createIntermediateGroups = project.options.createIntermediateGroups
 
         let parentPath = path.parent()
+
+        guard !isInsideSyncedFolder(path: path) else {
+            return getFileReference(path: path, inPath: basePath, sourceTree: .sourceRoot)
+        }
+
         let fileReference = getFileReference(path: path, inPath: parentPath)
+
         let parentGroup = getGroup(
             path: parentPath,
             mergingChildren: [fileReference],
@@ -283,6 +289,19 @@ class SourceGenerator {
         }
     }
 
+    /// Whether the given path falls inside a target source configured as a synced folder.
+    /// Checks the project spec directly because configFiles are resolved before target sources
+    /// populate `syncedGroupsByPath`.
+    private func isInsideSyncedFolder(path: Path) -> Bool {
+        let relativePath = (try? path.relativePath(from: basePath)) ?? path
+        return project.targets.contains { target in
+            target.sources.contains { source in
+                let type = source.type ?? (project.options.defaultSourceDirectoryType ?? .group)
+                return type == .syncedFolder && relativePath.string.hasPrefix(source.path + "/")
+            }
+        }
+    }
+
     /// returns a default build phase for a given path. This is based off the filename
     private func getDefaultBuildPhase(for path: Path, targetType: PBXProductType) -> BuildPhaseSpec? {
         if let buildPhase = getFileType(path: path)?.buildPhase {
@@ -356,7 +375,7 @@ class SourceGenerator {
             groupReference = addObject(group)
             groupsByPath[path] = groupReference
 
-            if isTopLevelGroup {
+            if isTopLevelGroup && !isInsideSyncedFolder(path: path) {
                 rootGroups.insert(groupReference)
             }
         }
@@ -402,6 +421,8 @@ class SourceGenerator {
                     if child.isDirectory && !Xcode.isDirectoryFileWrapper(path: child) {
                         findExceptions(in: child)
                     }
+                } else if child.isDirectory && !Xcode.isDirectoryFileWrapper(path: child) {
+                    findExceptions(in: child)
                 } else {
                     exceptions.insert(child)
                 }

Tests/XcodeGenKitTests/SourceGeneratorTests.swift

@@ -415,7 +415,7 @@ class SourceGeneratorTests: XCTestCase {
                 try expect(exceptions.contains("Nested/b.swift")) == false
             }
 
-            $0.it("excludes entire subdirectory as single exception when no files in it are included") {
+            $0.it("excludes individual files in subdirectory when no files in it are included") {
                 let directories = """
                 Sources:
                   - a.swift
@@ -436,10 +436,11 @@ class SourceGeneratorTests: XCTestCase {
                 let exceptionSet = try unwrap(syncedFolder.exceptions?.first as? PBXFileSystemSynchronizedBuildFileExceptionSet)
                 let exceptions = try unwrap(exceptionSet.membershipExceptions)
 
-                // The whole directory should be a single exception entry, not each file within it
-                try expect(exceptions.contains("ExcludedDir")) == true
-                try expect(exceptions.contains("ExcludedDir/x.swift")) == false
-                try expect(exceptions.contains("ExcludedDir/y.swift")) == false
+                // Xcode does not recursively exclude directory contents from membershipExceptions,
+                // so individual files must be listed instead of the directory name
+                try expect(exceptions.contains("ExcludedDir")) == false
+                try expect(exceptions.contains("ExcludedDir/x.swift")) == true
+                try expect(exceptions.contains("ExcludedDir/y.swift")) == true
                 try expect(exceptions.contains("a.swift")) == false
             }
 
@@ -491,6 +492,34 @@ class SourceGeneratorTests: XCTestCase {
                 try expect(appGroup === testsGroup) == true
             }
 
+            $0.it("does not create duplicate group for configFiles inside synced folder") {
+                let directories = """
+                Sources:
+                  - a.swift
+                  - Config:
+                    - config.xcconfig
+                """
+                try createDirectories(directories)
+
+                let source = TargetSource(path: "Sources", type: .syncedFolder)
+                let target = Target(name: "Target1", type: .application, platform: .iOS, sources: [source])
+                let project = Project(
+                    basePath: directoryPath,
+                    name: "Test",
+                    targets: [target],
+                    configFiles: ["Debug": "Sources/Config/config.xcconfig"]
+                )
+
+                let pbxProj = try project.generatePbxProj()
+                let mainGroup = try pbxProj.getMainGroup()
+
+                let sourcesChildren = mainGroup.children.filter { $0.path == "Sources" || $0.name == "Sources" }
+                try expect(sourcesChildren.count) == 1
+
+                let syncedFolders = mainGroup.children.compactMap { $0 as? PBXFileSystemSynchronizedRootGroup }
+                try expect(syncedFolders.count) == 1
+            }
+
             $0.it("supports frameworks in sources") {
                 let directories = """
                 Sources: